1
|
Barkan R, Cooke I, Watson SA, Lau SCY, Strugnell JM. Chromosome-scale genome assembly of the tropical abalone (Haliotis asinina). Sci Data 2024; 11:999. [PMID: 39266538 PMCID: PMC11393055 DOI: 10.1038/s41597-024-03840-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024] Open
Abstract
Abalone (family Haliotidae) are an ecologically and economically significant group of marine gastropods that can be found in tropical and temperate waters. To date, only a few Haliotis genomes are available, all belonging to temperate species. Here, we provide the first chromosome-scale abalone genome assembly and the first reference genome of the tropical abalone Haliotis asinina. The combination of PacBio long-read HiFi sequencing and Dovetail's Omni-C sequencing allowed the chromosome-level assembly of this genome, while PacBio Isoform sequencing across five tissue types enabled the construction of high-quality gene models. This assembly resulted in 16 pseudo-chromosomes spanning over 1.12 Gb (98.1% of total scaffolds length), N50 of 67.09 Mb, the longest scaffold length of 105.96 Mb, and a BUSCO completeness score of 97.6%. This study identified 25,422 protein-coding genes and 61,149 transcripts. In an era of climate change and ocean warming, this genome of a heat-tolerant species can be used for comparative genomics with a focus on thermal resistance. This high-quality reference genome of H. asinina is a valuable resource for aquaculture, fisheries, and ecological studies.
Collapse
Affiliation(s)
- Roy Barkan
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.
| | - Ira Cooke
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811, Australia
| | - Sue-Ann Watson
- Biodiversity and Geosciences Program, Queensland Museum Tropics, Queensland Museum, Townsville, Queensland, 4810, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Sally C Y Lau
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| |
Collapse
|
2
|
Ma Z, Wu Y, Zhang Y, Zhang W, Jiang M, Shen X, Wu H, Chen X, Di G. Morphologic, cytometric, quantitative transcriptomic and functional characterisation provide insights into the haemocyte immune responses of Pacific abalone ( Haliotis discus hannai). Front Immunol 2024; 15:1376911. [PMID: 39015569 PMCID: PMC11250055 DOI: 10.3389/fimmu.2024.1376911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/31/2024] [Indexed: 07/18/2024] Open
Abstract
In recent years, the abalone aquaculture industry has been threatened by the bacterial pathogens. The immune responses mechanisms underlying the phagocytosis of haemocytes remain unclear in Haliotis discus hannai. It is necessary to investigate the immune mechanism in response to these bacterial pathogens challenges. In this study, the phagocytic activities of haemocytes in H. discus hannai were examined by flow cytometry combined with electron microscopy and transcriptomic analyses. The results of Vibrio parahaemolyticus, Vibrio alginolyticus and Staphylococcus aureu challenge using electron microscopy showed a process during phagosome formation in haemocytes. The phagocytic rate (PP) of S. aureus was higher than the other five foreign particles, which was about 63%. The PP of Vibrio harveyi was about 43%, the PP peak of V. alginolyticus in haemocyte was 63.7% at 1.5 h. After V. parahaemolyticus and V. alginolyticus challenge, acid phosphatase, alkaline phosphatase, total superoxide dismutase, lysozyme, total antioxidant capacity, catalase, nitric oxide synthase and glutathione peroxidase activities in haemocytes were measured at different times, differentially expressed genes (DEGs) were identified by quantitative transcriptomic analysis. The identified DEGs after V. parahaemolyticus challenge included haemagglutinin/amebocyte aggregation factor-like, supervillin-like isoform X4, calmodulin-like and kyphoscoliosis peptidase-like; the identified DEGs after V. alginolyticus challenge included interleukin-6 receptor subunit beta-like, protein turtle homolog B-like, rho GTPase-activating protein 6-like isoform X2, leukocyte surface antigen CD53-like, calponin-1-like, calmodulin-like, troponin C, troponin I-like isoform X4, troponin T-like isoform X18, tumor necrosis factor ligand superfamily member 10-like, rho-related protein racA-like and haemagglutinin/amebocyte aggregation factor-like. Some immune-related KEGG pathways were significantly up-regulated or down-regulated after challenge, including thyroid hormone synthesis, Th17 cell differentiation signalling pathway, focal adhesion, melanogenesis, leukocyte transendothelial migration, inflammatory mediator regulation of TRP channels, ras signalling pathway, rap1 signalling pathway. This study is the first step towards understanding the H. discus hannai immune system by adapting several tools to gastropods and providing a first detailed morpho-functional study of their haemocytes.
Collapse
Affiliation(s)
- Zeyuan Ma
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunlong Wu
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Zhang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weini Zhang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingmei Jiang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoyue Shen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hailian Wu
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinhua Chen
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Guilan Di
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
3
|
Liang Y, Carrillo-Baltodano AM, Martín-Durán JM. Emerging trends in the study of spiralian larvae. Evol Dev 2024; 26:e12459. [PMID: 37787615 DOI: 10.1111/ede.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.
Collapse
Affiliation(s)
- Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
4
|
Tshilate TS, Ishengoma E, Rhode C. Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae). Anim Genet 2024. [PMID: 38945682 DOI: 10.1111/age.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/23/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024]
Abstract
Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.
Collapse
Affiliation(s)
| | - Edson Ishengoma
- Department of Genetics, Stellenbosch University, Matieland, South Africa
- Mkwawa University College of Education, University of Dar es Salaam, Iringa, Tanzania
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| |
Collapse
|
5
|
Zhang Q, Huang J, Fu Y, Chen J, Wang W. Genome-wide identification and expression profiles of sex-related gene families in the Pacific abalone Haliotis discus hannai. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101205. [PMID: 38364653 DOI: 10.1016/j.cbd.2024.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
In recent years, members of the Dmrt family, TGF-β superfamily and Sox family have been recognized as crucial genes for sex determination/differentiation across diverse animal species. Nevertheless, knowledge regarding the abundance and potential functions of these genes in abalone remains limited. In this study, a total of 5, 10, and 7 members of the Dmrt family, the TGF-β superfamily and the Sox family, respectively, were identified in the Pacific abalone Haliotis discus hannai. Sequence characteristics, phylogenetic relationships and spatiotemporal expression profiles of these genes were investigated. Notably, HdDmrt-04 (Dmrt1/1L-like) emerged as a potential mollusc-specific gene with a preponderance for expression in the testis. Interestingly, none of the TGF-β superfamily members exhibited specific or elevated expression in the gonads, highlighting the need for further investigation into their role in abalone sex differentiation. The Sox proteins in H. discus hannai were categorized into 7 subfamilies: B1, B2, C, D, E, F, and H. Among them, HdSox-07 (SoxH-like) was observed to play a crucial role in testis development, while HdSox-03 (SoxB1-like) and HdSox-04 (SoxC-like) probably cooperate in abalone ovary development. Taken together, the results of the present study suggested that HdDmrt-04 and HdSox-07 can be used as male-specific markers for gonad differentiation in H. discus hannai and imply conservation of their functions across invertebrates and vertebrates. Our findings provide new insights into the evolution and genetic structure of the Dmrt family, the TGF-β superfamily and the Sox family in abalone and pave the way for a deeper understanding of sex differentiation in gastropods.
Collapse
Affiliation(s)
- Qian Zhang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Jianfang Huang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China
| | - Yangtao Fu
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jianming Chen
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
| | - Wei Wang
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou 350108, China; Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Minjiang University, Fuzhou 350108, China.
| |
Collapse
|
6
|
Chen Y, Zhang W, Chen X, Zhang T, Wei H, Huang J, Fan C, Cai M, Wang Y, Zhang Z. Identification, diversity, and evolution analysis of Commd gene family in Haliotis discus hannai and immune response to biotic and abiotic stresses. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109533. [PMID: 38575039 DOI: 10.1016/j.fsi.2024.109533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The Commd (Copper Metabolism gene MURR1 Domain) family genes play crucial roles in various biological processes, including copper and sodium transport regulation, NF-κB activity, and cell cycle progression. Their function in Haliotis discus hannai, however, remains unclear. This study focused on identifying and analyzing the Commd genes in H. discus hannai, including their gene structure, phylogenetic relationships, expression profiles, sequence diversity, and alternative splicing. The results revealed significant homology between H. discus hannai's Commd genes and those of other mollusks. Both transcriptome quantitative analysis and qRT-PCR demonstrated the responsiveness of these genes to heat stress and Vibrio parahaemolyticus infection. Notably, alternative splicing analysis revealed that COMMD2, COMMD4, COMMD5, and COMMD7 produce multiple alternative splice variants. Furthermore, sequence diversity analysis uncovered numerous missense mutations, specifically 9 in COMMD5 and 14 in COMMD10. These findings contribute to expanding knowledge on the function and evolution of the Commd gene family and underscore the potential role of COMMD in the innate immune response of H. discus hannai. This research, therefore, offers a novel perspective on the molecular mechanisms underpinning the involvement of Commd genes in innate immunity, paving the way for further explorations in this field.
Collapse
Affiliation(s)
- Yuping Chen
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenxin Zhang
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Chen
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tao Zhang
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huina Wei
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianpeng Huang
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Fan
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingyi Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, 361021, China.
| | - Ziping Zhang
- State Key Laboratory of Mariculture Breeding, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
7
|
Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U. The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes. Front Genet 2023; 14:1244493. [PMID: 37829276 PMCID: PMC10565955 DOI: 10.3389/fgene.2023.1244493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group's main clades and whose origin has been dated more than 400 million years ago. Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades. Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system. Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
Collapse
Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Julia Heintz
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Ulf Jondelius
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| |
Collapse
|
8
|
Kim MA, Kim TH, Kannan P, Kho KH, Park K, Sohn YC. Functional Characterization of Gonadotropin-Releasing Hormone and Corazonin Signaling Systems in Pacific Abalone: Toward Reclassification of Invertebrate Neuropeptides. Neuroendocrinology 2023; 114:64-89. [PMID: 37703838 DOI: 10.1159/000533662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
INTRODUCTION The proposed evolutionary origins and corresponding nomenclature of bilaterian gonadotropin-releasing hormone (GnRH)-related neuropeptides have changed tremendously with the aid of receptor deorphanization. However, the reclassification of the GnRH and corazonin (CRZ) signaling systems in Lophotrochozoa remains unclear. METHODS We characterized GnRH and CRZ receptors in the mollusk Pacific abalone, Haliotis discus hannai (Hdh), by phylogenetic and gene expression analyses, bioluminescence-based reporter, Western blotting, substitution of peptide amino acids, in vivo neuropeptide injection, and RNA interference assays. RESULTS Two Hdh CRZ-like receptors (Hdh-CRZR-A and Hdh-CRZR-B) and three Hdh GnRH-like receptors (Hdh-GnRHR1-A, Hdh-GnRHR1-B, and Hdh-GnRHR2) were identified. In phylogenetic analysis, Hdh-CRZR-A and -B grouped within the CRZ-type receptors, whereas Hdh-GnRHR1-A/-B and Hdh-GnRHR2 clustered within the GnRH/adipokinetic hormone (AKH)/CRZ-related peptide-type receptors. Hdh-CRZR-A/-B and Hdh-GnRHR1-A were activated by Hdh-CRZ (pQNYHFSNGWHA-NH2) and Hdh-GnRH (pQISFSPNWGT-NH2), respectively. Hdh-CRZR-A/-B dually coupled with the Gαq and Gαs signaling pathways, whereas Hdh-GnRHR1-A was linked only with Gαq signaling. Analysis of substituted peptides, [I2S3]Hdh-CRZ and [N2Y3H4]Hdh-GnRH, and in silico docking models revealed that the N-terminal amino acids of the peptides are critical for the selectivity of Hdh-CRZR and Hdh-GnRHR. Two precursor transcripts for Hdh-CRZ and Hdh-GnRH peptides and their receptors were mainly expressed in the neural ganglia, and their levels increased in starved abalones. Injection of Hdh-CRZ peptide into abalones decreased food consumption, whereas Hdh-CRZR knockdown increased food consumption. Moreover, Hdh-CRZ induced germinal vesicle breakdown in mature oocytes. CONCLUSION Characterization of Hdh-CRZRs and Hdh-GnRHRs and their cognate peptides provides new insight into the evolutionary route of GnRH-related signaling systems in bilaterians.
Collapse
Affiliation(s)
- Mi Ae Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Tae Ha Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
| |
Collapse
|
9
|
Zou Y, Xu X, Xiao X, Wang Y, Yang H, Zhang Z. Genome-wide identification and characterization of Toll-like receptors (TLR) genes in Haliotis discus hannai, H. rufescens, and H. laevigata. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108728. [PMID: 37011737 DOI: 10.1016/j.fsi.2023.108728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/26/2023] [Accepted: 03/31/2023] [Indexed: 05/22/2023]
Abstract
Toll-like receptors (TLRs) play essential roles in the innate immune system and have been extensively studied in mollusks. In this study, through a genome-wide search, TLR genes were identified as 29 in Haliotis discus hannai, 33 in H. rufescens, and 16 in H. laevigata. Domain analysis indicated that these TLR genes contain leucine-rich repeat (LRR) and Toll/IL-1 receptor (TIR) domains and exons ranging from 1 to 5. Polymorphism analysis showed that the TLRs in abalones did not have high diversities with 143 SNPs and no Indel in H. discus hannai, 92 SNPs and 3 Indels together with 6 missense mutations in H. rufescens, and no SNP or Indel in H. laevigata. The expression of 8 TLR genes in H. discus hannai was confirmed in the hepatopancreas, gill, hemolymph, gonads, intestine, muscle, and mantle. The expression of five TLR genes (out of 8) in gills (p < 0.05), three in hepatopancreas (p < 0.05), and three in hemolymph (p < 0.05) was upregulated separately in response to the infection caused by Vibrio parahaemolyticus. The findings in this study would contribute to a better understanding of the molecular immune mechanism of H. discus hannai against stimulation by V. parahaemolyticus and provide a basis for the study of TLRs in abalones.
Collapse
Affiliation(s)
- Yuelian Zou
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Xu
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaotian Xiao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, 361021, China
| | - Huiping Yang
- School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32615, USA
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
10
|
Tshilate TS, Ishengoma E, Rhode C. A first annotated genome sequence for Haliotis midae with genomic insights into abalone evolution and traits of economic importance. Mar Genomics 2023; 70:101044. [PMID: 37196472 DOI: 10.1016/j.margen.2023.101044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 05/19/2023]
Abstract
Haliotis midae or "perlemoen" is one of five abalone species endemic to South Africa, and being palatable, the only commercially important abalone species with a high international demand. The higher demand for this abalone species has resulted in the decrease of natural stocks due to overexploitation by capture fisheries and poaching. Facilitating aquaculture production of H. midae should assist in minimising the pressure on the wild populations. Here, the draft genome of H. midae has been sequenced, assembled, and annotated. The draft assembly resulted in a total length of 1.5 Gb, contig N50 of 0.238 Mb, scaffold N50 of 0. 238 Mb and GC level of 40%. Gene annotation, combining ab initio and evidence-based pipelines identified 52,280 genes with protein coding potential. The genes identified were used to predict orthologous genes shared among the four other abalone species (H. laevigata, H. rubra, H. discus hannai and H. rufescens) and 4702 orthologous genes were shared across the five species. Among the orthologous genes in abalones, single copy genes were further analysed for signatures of selection and several molecular regulatory proteins involved in developmental functions were found to be under positive selection in specific abalone lineages. Furthermore, whole genome SNP-based phylogenomic assessment was performed to confirm the evolutionary relationship among the considered abalone species with draft genomes, reaffirming that H. midae is closely related to the Australian Greenlip (H. laevigata) and Blacklip (H. rubra). The study assists in the understanding of genes related to various biological systems underscoring the evolution and development of abalones, with potential applications for genetic improvement of commercial stocks.
Collapse
Affiliation(s)
- Thendo S Tshilate
- Department of Genetics, Stellenbosch University, Private bag X1, Matieland 7602, South Africa
| | - Edson Ishengoma
- Department of Genetics, Stellenbosch University, Private bag X1, Matieland 7602, South Africa; Mkwawa University College of Education, University of Dar es Salaam, P.O. BOX 2513, Iringa, Tanzania
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private bag X1, Matieland 7602, South Africa.
| |
Collapse
|
11
|
Noh ES, Subramaniyam S, Cho S, Kim YO, Park CJ, Lee JH, Nam BH, Shin Y. Genotyping of Haliotis discus hannai and machine learning models to predict the heat resistant phenotype based on genotype. Front Genet 2023; 14:1151427. [PMID: 37065481 PMCID: PMC10102348 DOI: 10.3389/fgene.2023.1151427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Geoje, Republic of Korea
| | | | - Sunghyun Cho
- Research and Development Center, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Geoje, Republic of Korea
| | - Choul-Ji Park
- Fisheries Seed and Breeding Research Institute, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jeong-Ho Lee
- Fish Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Geoje, Republic of Korea
| | - Younhee Shin
- Research and Development Center, Yongin-si, Gyeonggi-do, Republic of Korea
- *Correspondence: Younhee Shin,
| |
Collapse
|
12
|
Hirase S, Sekino M, Hara M, Kikuchi K. Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation. Ecol Evol 2023; 13:e9816. [PMID: 36818538 PMCID: PMC9936805 DOI: 10.1002/ece3.9816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/21/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
The genetic basis of speciation in free-spawning marine invertebrates is poorly understood. Although gene copy number variations (GCNVs) and nucleotide variations possibly trigger the speciation of these organisms, empirical evidence for such a hypothesis is limited. In this study, we searched for genomic signatures of GCNVs that may contribute to the speciation of Western Pacific abalone species. Whole-genome sequencing data suggested the existence of significant amounts of GCNVs in closely related abalones, Haliotis discus and H. madaka, in the early phase of speciation. In addition, the degree of interspecies genetic differentiation in the genes where GCNVs were estimated was higher than that in other genes, suggesting that nucleotide divergence also accumulates in the genes with GCNVs. GCNVs in some genes were also detected in other related abalone species, suggesting that these GCNVs are derived from both ancestral and de novo mutations. Our findings suggest that GCNVs have been accumulated in the early phase of free-spawning abalone speciation.
Collapse
Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life SciencesThe University of TokyoShizuokaJapan
| | - Masashi Sekino
- Bioinformatics and Biosciences Division, Fisheries Resources InstituteJapan Fisheries Research and Education AgencyYokohamaJapan
| | - Motoyuki Hara
- Tohoku Ecosystem‐Associated Marine SciencesTohoku UniversitySendaiJapan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life SciencesThe University of TokyoShizuokaJapan
| |
Collapse
|
13
|
Griffiths JS, Sahasrabudhe RM, Marimuthu MPA, Chumchim N, Nguyen OH, Beraut E, Escalona M, Whitehead A. A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics. J Hered 2022; 113:673-680. [PMID: 36190478 PMCID: PMC9709998 DOI: 10.1093/jhered/esac047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/05/2022] [Indexed: 11/14/2022] Open
Abstract
Red abalone, Haliotis rufescens, are herbivorous marine gastropods that primarily feed on kelp. They are the largest and longest-lived of abalone species with a range distribution in North America from central Oregon, United States, to Baja California, MEX. Recently, red abalone have been in decline as a consequence of overharvesting, disease, and climate change, resulting in the closure of the commercial fishery in the 1990s and the recreational fishery in 2018. Protecting this ecologically and economically important species requires an understanding of their current population dynamics and connectivity. Here, we present a new red abalone reference genome as part of the California Conservation Genomics Project (CCGP). Following the CCGP genome strategy, we used Pacific Biosciences HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly. The assembly comprises 616 scaffolds for a total size of 1.3 Gb, a scaffold N50 of 45.7 Mb, and a BUSCO complete score of 97.3%. This genome represents a significant improvement over a previous assembly and will serve as a powerful tool for investigating seascape genomic diversity, local adaptation to temperature and ocean acidification, and informing management strategies.
Collapse
Affiliation(s)
- Joanna S Griffiths
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| | - Ruta M Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, 95616, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, 95616, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, 95616, United States
| | - Oanh H Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California Davis, Davis, CA, 95616, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| |
Collapse
|
14
|
Orland C, Escalona M, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Beraut E, Marshman B, Moore J, Raimondi P, Shapiro B. A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii. J Hered 2022; 113:665-672. [PMID: 35567593 PMCID: PMC9709981 DOI: 10.1093/jhered/esac024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
The once abundant black abalone, Haliotis cracherodii, is a large, long-lived grazing marine mollusk that inhabits the rocky intertidal along the coast of California. The species has experienced dramatic declines since the mid-1980s largely due to the fatal bacterial disease called withering syndrome, leading to the collapse of an economically important fishery and to its inclusion into the IUCN listing as a critically endangered species. In some places impacted by the disease, populations of black abalone have declined by more than 90%, prompting population crashes associated with very little recruitment of new individuals and changes to intertidal communities. Habitats that were dominated by crustose coralline algae and bare rock have become dominated instead by fleshy algae and sessile invertebrates. Here, we present the first high-quality black abalone reference genome, assembled with PacBio HiFi long-reads and assembled with Dovetail Omni-C data to generate a scaffold-level assembly. The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans.
Collapse
Affiliation(s)
- Chloé Orland
- Address correspondence to C. Orland at the address above, or e-mail:
| | | | - Ruta Sahasrabudhe
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Mohan P A Marimuthu
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Oanh Nguyen
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Eric Beraut
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blythe Marshman
- Marine Laboratory, University of California Davis, Davis, CA, USA
| | - James Moore
- Marine Laboratory, University of California Davis, Davis, CA, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
15
|
Vargas-Peralta CE, Araneda C, Galindo-Sánchez CE, Larraín MA, Del Río-Portilla MA, Lafarga-De la Cruz F. Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M. Evolution of EGF-like and Zona pellucida domains containing shell matrix proteins in mollusks. Mol Biol Evol 2022; 39:6633355. [PMID: 35796746 PMCID: PMC9290575 DOI: 10.1093/molbev/msac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several types of shell matrix proteins (SMPs) have been identified in molluskan shells. Their diversity is the consequence of various molecular processes, including domain shuffling and gene duplication. However, the evolutionary origin of most SMPs remains unclear. In this study, we investigated the evolutionary process EGF-like and zona pellucida (ZP) domains containing SMPs. Two types of the proteins (EGF-like protein (EGFL) and EGF-like and ZP domains containing protein (EGFZP)) were found in the pearl oyster, Pinctada fucata. In contrast, only EGFZP was identified in the gastropods. Phylogenetic analysis and genomic arrangement studies showed that EGFL and EGFZP formed a clade in bivalves, and their encoding genes were localized in tandem repeats on the same scaffold. In P. fucata, EGFL genes were expressed in the outer part of mantle epithelial cells are related to the calcitic shell formation. However, in both P. fucata and the limpet Nipponacmea fuscoviridis, EGFZP genes were expressed in the inner part of the mantle epithelial cells are related to aragonitic shell formation. Furthermore, our analysis showed that in P. fucata, the ZP domain interacts with eight SMPs that have various functions in the nacreous shell mineralization. The data suggest that the ZP domain can interact with other SMPs, and EGFL evolution in pterimorph bivalves represents an example of neo-functionalization that involves the acquisition of a novel protein through gene duplication.
Collapse
Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie 517-0404, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| |
Collapse
|
17
|
Kim J, Kim HS, Choi JP, Kim MS, Woo S, Kim Y, Jo Y, Yum S, Bhak J. Chromosome-Level Genome Assembly of the Butter Clam Saxidomus purpuratus. Genome Biol Evol 2022; 14:6650251. [PMID: 35881514 PMCID: PMC9337622 DOI: 10.1093/gbe/evac106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 11/12/2022] Open
Abstract
Herein, we provide the first whole-genome sequence of the purple butter clam (Saxidomus purpuratus), an economically important bivalve shellfish. Specifically, we sequenced and de novo assembled the genome of Sa. purpuratus based on PromethION long reads and Hi-C data. The 978-Mb genome of Sa. purpuratus comprises 19 chromosomes with 36,591 predicted protein-coding genes. The N50 length of Sa. purpuratus genome is 52 Mb, showing the highest continuous assembly among bivalve genomes. The Benchmarking by Universal Single-Copy Orthologs assessment indicated that 95.07% of complete metazoan universal single-copy orthologs (n = 954) were present in the assembly. Approximately 51% of Sa. purpuratus genome comprises repetitive sequences. Based on the high-quality Sa. purpuratus genome, we resolved half of the immune-associated genes, namely, scavenger receptor (SR) proteins, which are collinear to those in the closely related Cyclina sinensis genome. This finding suggested a high degree of conservation among immune-associated genes. Twenty-two (19%) SR proteins are tandemly duplicated in Sa. purpuratus genome, suggesting putative convergence evolution. Overall, Sa. purpuratus genome provides a new resource for the discovery of economically important traits and immune-response genes.
Collapse
Affiliation(s)
- Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28190, Republic of Korea
| | - Hui-Su Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae-Pil Choi
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28190, Republic of Korea
| | - Min Sun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28190, Republic of Korea
| | - Seonock Woo
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49 111, Republic of Korea
| | - Yeonghye Kim
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Yejin Jo
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Republic of Korea
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Republic of Korea.,KIOST School, University of Science and Technology, Geoje 53201, Republic of Korea
| | - Jong Bhak
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28190, Republic of Korea.,Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea.,Clinomics, Inc., Ulsan 44919, Republic of Korea
| |
Collapse
|
18
|
Zhang X, Guo M, Sun Y, Wang Y, Zhang Z. Transcriptomic analysis and discovery of genes involving in enhanced immune protection of Pacific abalone (Haliotis discus hannai) in response to the re-infection of Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2022; 125:128-140. [PMID: 35523358 DOI: 10.1016/j.fsi.2022.04.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Traditionally, invertebrates were thought to lack immune memory owing to a lack of acquired immune-related factors such as immunoglobulin. Nonetheless, with the in-depth consideration of invertebrate immune priming, scholars have gradually realized that the immune defenses of invertebrates are more complex than previously imagined. In the current investigation, the survival rate of Vibrio parahaemolyticus re-infected Haliotis discus hannai (VV group) was significantly different from the other groups (p < 0.05), indicating that an enhanced immune response may commence after first exposure to the same strain of V. parahaemolyticus. The transcriptome profiles of hemocytes obtained 102,052 unigenes, and 27,449 of them were annotated successfully. Venn diagram analysis showed that 2832 DEGs commonly responded to the first and second immune responses. 1734 "immune response genes" and 1460 "potential immune-enhancing genes" were also identified. A comparison of both "immune response genes" and "potential immune-enhancing genes" revealed 1019 immune-enhancing regulatory genes and 281 essential immune-enhancing genes. According to the KEGG enrichment analysis results of ERGs and EEGs, classical immune-related signaling pathways, such as NF-kappa B signaling pathway, NOD-like receptor signaling pathway, IL-17 signaling pathway, and TLR signaling pathway were significantly enriched, indicating that they were all involved in the response to V. parahaemolyticus re-infection and were likely dominant in the immune enhancement process of H. discus hannai hemocytes. The intermolecular interactions generated by Cytoscape after re-infection of V. parahaemolyticus appear more intuitively to demonstrate that hemocytes regulation was not an independent process, but rather an intricate regulatory network. H. discus hannai demonstrated enhanced immunological activity after re-infection with V. parahaemolyticus, showing immune memory in hemocytes. The current study's findings have broadened the study of immune enhancement in invertebrates and laid the framework for future research into the molecular mechanism of immune enhancement in abalones.
Collapse
Affiliation(s)
- Xin Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China
| | - Mingxing Guo
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yulong Sun
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
19
|
Morino Y. Dynamic evolutionary history of spiralian-specific TALE homeobox genes in mollusks. Dev Growth Differ 2022; 64:198-209. [PMID: 35441397 DOI: 10.1111/dgd.12779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
Homeobox genes play essential roles in the early development of many animals. Although the repertoire of most homeobox genes, including three amino acid loop extension (TALE)-type homeobox genes, is conserved in animals, spiralian-TALE (SPILE) genes are a notable exception. In this study, SPILE genes were extracted from the genomic data of 22 mollusk species and classified into four clades (-A/C, -B, -D, and -E) to determine which SPILE genes exhibit dynamic repertoire changes. While SPILE-D and -E duplications were rarely observed, SPILE-B duplication was observed in the bivalve lineage and SPILE-A/C duplication was observed in multiple clades. Conversely, most or all SPILE genes were lost in cephalopods and in some gastropod lineages. SPILE gene expression patterns were also analyzed in multiple mollusk species using publicly available RNA-seq data. The majority of SPILE genes examined, particularly those in the A/C- and B-clades, were specifically expressed during early development, suggesting that most SPILE genes exert specific roles in early development. This comprehensive cataloging and characterization revealed a dynamic evolutionary history, including SPILE-A/C and -B gene duplications and the loss of SPILE genes in several lineages. Furthermore, this study provides a useful resource for studying the molecular mechanism of spiralian early development and the evolution of young and lineage-specific transcription factors.
Collapse
Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| |
Collapse
|
20
|
Carlisle JA, Glenski MA, Swanson WJ. Recurrent Duplication and Diversification of Acrosomal Fertilization Proteins in Abalone. Front Cell Dev Biol 2022; 10:795273. [PMID: 35465314 PMCID: PMC9022041 DOI: 10.3389/fcell.2022.795273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Reproductive proteins mediating fertilization commonly exhibit rapid sequence diversification driven by positive selection. This pattern has been observed among nearly all taxonomic groups, including mammals, invertebrates, and plants, and is remarkable given the essential nature of the molecular interactions mediating fertilization. Gene duplication is another important mechanism that facilitates the generation of molecular novelty through functional divergence. Following duplication, paralogs may partition ancestral gene function (subfunctionalization) or acquire new roles (neofunctionalization). However, the contributions of duplication followed by sequence diversification to the molecular diversity of gamete recognition genes has been understudied in many models of fertilization. The marine gastropod mollusk abalone is a classic model for fertilization. Its two acrosomal proteins (lysin and sp18) are ancient gene duplicates with unique gamete recognition functions. Through detailed genomic and bioinformatic analyses we show how duplication events followed by sequence diversification has played an ongoing role in the evolution of abalone acrosomal proteins. The common ancestor of abalone had four members of its acrosomal protein family in a tandem gene array that repeatedly experienced positive selection. We find that both sp18 paralogs contain positively selected sites located in different regions of the paralogs, suggestive of functional divergence where selection acted upon distinct binding interfaces in each paralog. Further, a more recent species-specific duplication of both lysin and sp18 in the European abalone H. tuberculata is described. Despite clade-specific acrosomal protein paralogs, there are no concomitant duplications of egg coat proteins in H. tuberculata, indicating that duplication of egg proteins per se is not responsible for retention of duplicated acrosomal proteins. We hypothesize that, in a manner analogous to host/pathogen evolution, sperm proteins are selected for increased diversity through extensive sequence divergence and recurrent duplication driven by conflict mechanisms.
Collapse
Affiliation(s)
- J. A. Carlisle
- Genome Sciences Department, University of Washington Medical School, Seattle, WA, United States
- *Correspondence: J. A. Carlisle,
| | - M. A. Glenski
- Department of Biology, Gonzaga University, Spokane, WA, United States
| | - W. J. Swanson
- Genome Sciences Department, University of Washington Medical School, Seattle, WA, United States
| |
Collapse
|
21
|
Sun Y, Zhang X, Wang Y, Zhang Z. Long-read RNA sequencing of Pacific abalone Haliotis discus hannai reveals innate immune system responses to environmental stress. FISH & SHELLFISH IMMUNOLOGY 2022; 122:131-145. [PMID: 35122948 DOI: 10.1016/j.fsi.2022.01.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Haliotis discus hannai is a commercially important mollusk species, and the abalone aquaculture sector has been jeopardized by deteriorating environmental circumstances such as bacterial infection and thermal stress during the hot summers. However, due to a paucity of genetic information, such as transcriptome resources, our understanding of their stress adaptation is restricted. In this research, using single-molecule long-read (SMRT) sequencing technology, a library composed of ten tissues (i.e., haemocytes, gills, muscle, hepatopancreas, digestive tract, mantle, mucous gland, ovary, testis and head) was constructed and sequenced. In all, 41,855 high-quality unique transcripts, among which 24,778 were successfully annotated. Additionally, 13,463 SSRs, 1,169 transcription factors, and 18,124 lncRNAs were identified in H. discus hannai transcriptome. Furthermore, multiple immune-related transcripts were identified according to KEGG annotation, and a portion of these transcripts were mapped into several classical immune-related pathways, including the PI3K-AKT signaling pathway and Toll-like receptor signaling pathway. Additionally, 24 typical sequences related to the immunity pathway were detected by RT-PCR; the results showed that most of the immune-related genes showed significantly high expression at 72 h after bacterial challenges and thermal stress, especially the expression level of genes in gills was significantly higher than that in haemocytes under V. parahaemolyticus stress at 24 h. At the same time. The analysis of alternative splicing identified several innate immunity-related functions genes, including CD109 and caspase 2. These results suggest that the complex immune system, particularly the powerful innate immunity system, was crucial for H. discus hannai response to numerous environmental challenges.
Collapse
Affiliation(s)
- Yulong Sun
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fisheries College, Jimei University, Xiamen, 361021, China
| | - Xin Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fisheries College, Jimei University, Xiamen, 361021, China
| | - Yilei Wang
- Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Ziping Zhang
- College of Marine Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
22
|
Zhang Y, Mao F, Xiao S, Yu H, Xiang Z, Xu F, Li J, Wang L, Xiong Y, Chen M, Bao Y, Deng Y, Huo Q, Zhang L, Liu W, Li X, Ma H, Zhang Y, Mu X, Liu M, Zheng H, Wong NK, Yu Z. Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1078-1091. [PMID: 35091095 DOI: 10.1016/j.gpb.2021.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene Antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical C. hongkongensis and symmetrical Pinctada fucata in their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.
Collapse
Affiliation(s)
- Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fan Mao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Zhiming Xiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fei Xu
- CAS Key Laboratory of Experimental Marine Biology, Center for Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Yuanyan Xiong
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Mengqiu Chen
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yuewen Deng
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Quan Huo
- Hebei Key Laboratory of Applied Chemistry, College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066044, China
| | - Lvping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Wenguang Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Haitao Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yuehuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiyu Mu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101301, China.
| | - Nai-Kei Wong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Pharmacology, Shantou University Medical College, Shantou 515041, China.
| | - Ziniu Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| |
Collapse
|
23
|
Jia Y, Xu F, Liu X. Duplication and subsequent functional diversification of aquaporin family in Pacific abalone Haliotis discus hannai. Mol Phylogenet Evol 2022; 168:107392. [PMID: 35033672 DOI: 10.1016/j.ympev.2022.107392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 09/22/2021] [Accepted: 11/12/2021] [Indexed: 01/29/2023]
Abstract
Aquaporins (AQPs) are a group of proteins that evolved to mediate specific permeation of water and other small solutes, playing important roles in osmoregulation and nutrition, especially for aquatic animals. Genome-wide characterization of the AQP family in a typical mollusc, Pacific abalone, suggested that tandem duplication and retroduplication led to the dramatic expansion and diversification of AQP genes. Structural analysis indicated that tandem duplicated AQPs showed abnormal characteristics. The conserved amino acids in the key site of the Ar/R region were replaced by the others. These substitutions altered the pore diameter and properties of the inner surface and could accommodate the pass through of other molecules except water. Functional analysis indicated that abnormal Ar/R region of the tandemly adjacent members led to the different permeability, suggesting the neofunctionalization of tandemly duplicated genes. Mutation analysis indicated that at the key site of Ar/R region, just a single amino acid substitute could alter the permeability of HdAQPs, further explaining the mechanism of neofunctionalization between the tandem duplicated HdAQPs. Our observations provided strong evidence that duplication and subsequent neofunctionalization have led to structural and functional diversity of AQPs in Pacific abalone, providing insights into the evolution of AQPs in molluscs.
Collapse
Affiliation(s)
- Yanglei Jia
- Fishery College of Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Fei Xu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Xiao Liu
- Fishery College of Zhejiang Ocean University, Zhoushan, Zhejiang, China.
| |
Collapse
|
24
|
Zou Y, Xu X, Hu Q, Wang Y, Yang H, Zhang Z. Identification and diversity of fibrinogen-related protein (FREP) gene family in Haliotis discus hannai, H. rufescens, and H. laevigata and their responses to Vibrio parahemolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2021; 119:613-622. [PMID: 34740769 DOI: 10.1016/j.fsi.2021.10.041] [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: 08/26/2021] [Revised: 10/06/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Fibrinogen-related proteins (FREPs) are distributed universally in vertebrates and invertebrates. These proteins contain fibrinogen-like (FBG) domains in their C-terminal region and involve in immune responses and other aspects of physiology in invertebrates. In this study, 54 proteins that contain FBG domains or a fibrinogen_c domain were identified in Haliotis discus hannai. Comparatively, 88 and 63 FREPs were identified from the genomes of H. rufescens and H. laevigata. Most FREPs of abalones had a conserved motif containing a bound calcium ion site and a second conserved motif containing a polymerization pocket site. By sequence analysis, 394 SNPs and 11 Indels were identified in 20 FREP genes of the whole genome of H. discus hannai; 992 SNPs and 42 Indels were found in 64 FREPs of H. rufescens, and 192 SNPs and 12 Indels were found in 21 FREPs of H. laevigata. Among these SNPs, 92 missense mutation sites were identified in 26 FREP genes of H. rufescens, and 12 were identified in 8 FREP genes of H. laevigata. Due to the poor genomic integrity, annotations of the SNPs or Indels in H. discus hannai did not yield missense mutant sites. FREP genes with polymorphisms were ubiquitously expressed in all the tested tissues; however, the expression is lowest in the hemolymph. In response to Vibrio parahemolyticus infection, expression of FREP genes was significantly upregulated at different exposure times in gills, hepatopancreas, and hemolymph in H. discus hannai. Overall, this study documented the FREP genes of abalones and shed light on the role of FREPs in the innate immune system of these aquaculture species for the prevention and control of diseases.
Collapse
Affiliation(s)
- Yuelian Zou
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Xu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qilin Hu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yilei Wang
- College of Fisheries, Jimei University, Xiamen, 361021, China
| | - Huiping Yang
- School of Forest Resources and Conservation, IFAS, University of Florida, 7922 NW 71st Street, Gainesville, FL, 32615, USA
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
25
|
Hirase S, Yamasaki YY, Sekino M, Nishisako M, Ikeda M, Hara M, Merilä J, Kikuchi K. Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates. Mol Biol Evol 2021; 38:4683-4699. [PMID: 34311468 PMCID: PMC8557453 DOI: 10.1093/molbev/msab194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.
Collapse
Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masashi Sekino
- Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masato Nishisako
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Minoru Ikeda
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Motoyuki Hara
- Tohoku Ecosystem-Associated Marine Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Division of Ecology and Biodiversity, Faculty of Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
| |
Collapse
|
26
|
NPF activates a specific NPF receptor and regulates food intake in Pacific abalone Haliotis discus hannai. Sci Rep 2021; 11:20912. [PMID: 34686694 PMCID: PMC8536682 DOI: 10.1038/s41598-021-00238-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/07/2021] [Indexed: 01/13/2023] Open
Abstract
Neuropeptides function through G protein-coupled receptors (GPCRs) with high specificity, implying a significant degree of neuropeptide-GPCR coevolution. However, potential neuropeptide signaling systems in non-chordates are relatively elusive. We determined the specificity of the neuropeptide F (Hdh-NPF) signaling system with a cognate receptor (Hdh-NPFR) in the Pacific abalone, Haliotis discus hannai. Phylogenetic and exon–intron arrangement analyses of bilaterian NPF and the chordate ortholog NPY with their receptor sequences revealed a likely common ancestor, and Hdh-NPFR was similar to the NPYR2 subtype among the NPYR1, NPYR2, and NPYR5 subtypes. Among four Hdh-NPFR-related receptors, Hdh-NPFR specifically responded to Hdh-NPF peptide, supported by the dose–response luciferase reporter curve, intracellular Ca2+ mobilization, and phosphorylation of ERK1/2 and its inhibition with a protein kinase C inhibitor. Peptide fragmentations and shuffling of Hdh-NPF with human NPY could not activate the cellular response of Hdh-NPFR. Three-dimensional in silico modeling suggested that interaction of Hdh-NPF C-terminal amino acids with the extracellular loops of Hdh-NPFR is critical for Hdh-NPFR activation. In vivo injection of Hdh-NPF peptide increased food consumption, and knockdown of Hdh-NPF expression decreased food consumption in Pacific abalone. These findings provide evidence for co-evolution of the NPF/Y ligand-receptor system, enabling further research on mollusk orexigenic neuropeptides.
Collapse
|
27
|
Phuangphong S, Tsunoda J, Wada H, Morino Y. Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage. EvoDevo 2021; 12:11. [PMID: 34663437 PMCID: PMC8524836 DOI: 10.1186/s13227-021-00181-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates. Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-021-00181-2.
Collapse
Affiliation(s)
- Supanat Phuangphong
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Jumpei Tsunoda
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| |
Collapse
|
28
|
Gim JA, Baek KW, Hah YS, Choo HJ, Kim JS, Yoo JI. Draft genome of Semisulcospira libertina, a species of freshwater snail. Genomics Inform 2021; 19:e32. [PMID: 34638179 PMCID: PMC8510874 DOI: 10.5808/gi.21039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.
Collapse
Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, Korea University Guro Hospital, Korea University College of Medicine, Seoul 08308, Korea
| | - Kyung-Wan Baek
- Department of Physical Education, Gyeongsang National University, Jinju 52727, Korea.,Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea
| | - Young-Sool Hah
- Biomedical Research Institute, Gyeongsang National University Hospital, Jinju 52727, Korea
| | - Ho Jin Choo
- South Korea 4H Association, Seoul 05269, Korea
| | - Ji-Seok Kim
- Department of Physical Education, Gyeongsang National University, Jinju 52727, Korea
| | - Jun-Il Yoo
- Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea
| |
Collapse
|
29
|
Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
Collapse
Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|
30
|
Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
| |
Collapse
|
31
|
Liu F, Li Y, Yu H, Zhang L, Hu J, Bao Z, Wang S. MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. Nucleic Acids Res 2021; 49:D988-D997. [PMID: 33219670 PMCID: PMC7779068 DOI: 10.1093/nar/gkaa918] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/16/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.
Collapse
Affiliation(s)
- Fuyun Liu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Yuli Li
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hongwei Yu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| |
Collapse
|
32
|
Varney RM, Speiser DI, McDougall C, Degnan BM, Kocot KM. The Iron-Responsive Genome of the Chiton Acanthopleura granulata. Genome Biol Evol 2021; 13:evaa263. [PMID: 33320175 PMCID: PMC7850002 DOI: 10.1093/gbe/evaa263] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/27/2022] Open
Abstract
Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.
Collapse
Affiliation(s)
- Rebecca M Varney
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Carmel McDougall
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
- Alabama Museum of Natural History, Tuscaloosa, Alabama
| |
Collapse
|
33
|
Song K. Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas. Genome Biol Evol 2020; 12:1943-1952. [PMID: 32722758 PMCID: PMC7674689 DOI: 10.1093/gbe/evaa160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.
Collapse
Affiliation(s)
- Kai Song
- School of Mathematics and Statistics, Qingdao University, Shandong, China
| |
Collapse
|
34
|
Li Y, Nong W, Baril T, Yip HY, Swale T, Hayward A, Ferrier DEK, Hui JHL. Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome. BMC Genomics 2020; 21:713. [PMID: 33059600 PMCID: PMC7566022 DOI: 10.1186/s12864-020-07027-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/25/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. RESULTS Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. CONCLUSIONS The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.
Collapse
Affiliation(s)
- Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tobias Baril
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - Alexander Hayward
- Department of Conservation and Ecology, Penryn Campus, University of Exeter, Exeter, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Martine Laboratory, University of St. Andrews, St Andrews, UK.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| |
Collapse
|
35
|
Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
Collapse
Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| |
Collapse
|
36
|
Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S. The evo-devo of molluscs: Insights from a genomic perspective. Evol Dev 2020; 22:409-424. [PMID: 32291964 DOI: 10.1111/ede.12336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.
Collapse
Affiliation(s)
- Zhihui Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,The Sars-Fang Centre, Ocean University of China, Qingdao, China
| |
Collapse
|
37
|
Sun J, Chen C, Miyamoto N, Li R, Sigwart JD, Xu T, Sun Y, Wong WC, Ip JCH, Zhang W, Lan Y, Bissessur D, Watsuji TO, Watanabe HK, Takaki Y, Ikeo K, Fujii N, Yoshitake K, Qiu JW, Takai K, Qian PY. The Scaly-foot Snail genome and implications for the origins of biomineralised armour. Nat Commun 2020; 11:1657. [PMID: 32269225 PMCID: PMC7142155 DOI: 10.1038/s41467-020-15522-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanisms underlying the evolutionary diversification of biomineralised armour. Here, we present a high-quality whole-genome assembly and tissue-specific transcriptomic data, and show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors. Comparisons with other lophotrochozoan genomes imply that this biomineralisation toolkit is ancient, though expression patterns differ across major lineages. We suggest that the ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity for dynamic modification of the expression and positioning of toolkit elements across the genome.
Collapse
Affiliation(s)
- Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Norio Miyamoto
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, Portaferry, N. Ireland
- Senckenberg Museum, Frankfurt, Germany
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jack C H Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Weipeng Zhang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi Lan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Dass Bissessur
- Department for Continental Shelf, Maritime Zones Administration & Exploration, Ministry of Defence and Rodrigues, 2nd Floor, Belmont House, 12 Intendance Street, Port-Louis, 11328, Mauritius
| | - Tomo-O Watsuji
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
- Department of Food and Nutrition, Higashi-Chikushi Junior College, Kitakyusyu, Japan
| | - Hiromi Kayama Watanabe
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kazuho Ikeo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Nobuyuki Fujii
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ken Takai
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
| |
Collapse
|
38
|
Zheng X, Zhao S, Lei S, Ma R, Liu L, Xie Y, Shi X, Chen J. Cloning and characterization of a novel Lustrin A gene from Haliotis discus hannai. Comp Biochem Physiol B Biochem Mol Biol 2020; 240:110385. [DOI: 10.1016/j.cbpb.2019.110385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
|
39
|
Sun J, Mu H, Ip JCH, Li R, Xu T, Accorsi A, Sánchez Alvarado A, Ross E, Lan Y, Sun Y, Castro-Vazquez A, Vega IA, Heras H, Ituarte S, Van Bocxlaer B, Hayes KA, Cowie RH, Zhao Z, Zhang Y, Qian PY, Qiu JW. Signatures of Divergence, Invasiveness, and Terrestrialization Revealed by Four Apple Snail Genomes. Mol Biol Evol 2020; 36:1507-1520. [PMID: 30980073 PMCID: PMC6573481 DOI: 10.1093/molbev/msz084] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The family Ampullariidae includes both aquatic and amphibious apple snails. They are an emerging model for evolutionary studies due to the high diversity, ancient history, and wide geographical distribution. Insight into drivers of ampullariid evolution is hampered, however, by the lack of genomic resources. Here, we report the genomes of four ampullariids spanning the Old World (Lanistes nyassanus) and New World (Pomacea canaliculata, P. maculata, and Marisa cornuarietis) clades. The ampullariid genomes have conserved ancient bilaterial karyotype features and a novel Hox gene cluster rearrangement, making them valuable in comparative genomic studies. They have expanded gene families related to environmental sensing and cellulose digestion, which may have facilitated some ampullarids to become notorious invasive pests. In the amphibious Pomacea, novel acquisition of an egg neurotoxin and a protein for making the calcareous eggshell may have been key adaptations enabling their transition from underwater to terrestrial egg deposition.
Collapse
Affiliation(s)
- Jin Sun
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jack C H Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Alice Accorsi
- Howard Hughes Medical Institute, Kansas City, MO.,Stowers Institute for Medical Research, Kansas City, MO
| | - Alejandro Sánchez Alvarado
- Howard Hughes Medical Institute, Kansas City, MO.,Stowers Institute for Medical Research, Kansas City, MO
| | - Eric Ross
- Howard Hughes Medical Institute, Kansas City, MO.,Stowers Institute for Medical Research, Kansas City, MO
| | - Yi Lan
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanan Sun
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Alfredo Castro-Vazquez
- Instituto de Histología y Embriología (IHEM-CONICET), Mendoza, Argentina.,Instituto de Fisiología (FCM-UNCuyo), Mendoza, Argentina
| | - Israel A Vega
- Instituto de Histología y Embriología (IHEM-CONICET), Mendoza, Argentina.,Instituto de Fisiología (FCM-UNCuyo), Mendoza, Argentina
| | - Horacio Heras
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP. CONICET CCT La Plata-Universidad Nacional de La Plata (UNLP), La Plata, Argentina.,Facultad de Ciencias Naturales y Museo, UNLP, La Plata, Argentina
| | - Santiago Ituarte
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP. CONICET CCT La Plata-Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Bert Van Bocxlaer
- Centre national de la recherche scientifique (CNRS), UMR 8198 Evolution, Ecology, Paleotology, Université de Lille, Lille, France
| | | | - Robert H Cowie
- Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Pei-Yuan Qian
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| |
Collapse
|
40
|
Wilburn DB, Tuttle LM, Klevit RE, Swanson WJ. Indirect sexual selection drives rapid sperm protein evolution in abalone. eLife 2019; 8:e52628. [PMID: 31868593 PMCID: PMC6952181 DOI: 10.7554/elife.52628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022] Open
Abstract
Sexual selection can explain the rapid evolution of fertilization proteins, yet sperm proteins evolve rapidly even if not directly involved in fertilization. In the marine mollusk abalone, sperm secrete enormous quantities of two rapidly evolving proteins, lysin and sp18, that are stored at nearly molar concentrations. We demonstrate that this extraordinary packaging is achieved by associating into Fuzzy Interacting Transient Zwitterion (FITZ) complexes upon binding the intrinsically disordered FITZ Anionic Partner (FITZAP). FITZ complexes form at intracellular ionic strengths and, upon exocytosis into seawater, lysin and sp18 are dispersed to drive fertilization. NMR analyses revealed that lysin uses a common molecular interface to bind both FITZAP and its egg receptor VERL. As sexual selection alters the lysin-VERL interface, FITZAP coevolves rapidly to maintain lysin binding. FITZAP-lysin interactions exhibit a similar species-specificity as lysin-VERL interactions. Thus, tethered molecular arms races driven by sexual selection can generally explain rapid sperm protein evolution.
Collapse
Affiliation(s)
| | - Lisa M Tuttle
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Rachel E Klevit
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Willie J Swanson
- Department of Genome SciencesUniversity of WashingtonSeattleUnited States
| |
Collapse
|
41
|
Expression of Heat Shock Proteins in Thermally Challenged Pacific Abalone Haliotis discus hannai. Genes (Basel) 2019; 11:genes11010022. [PMID: 31878084 PMCID: PMC7016835 DOI: 10.3390/genes11010022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022] Open
Abstract
Summer mortality, caused by thermal conditions, is the biggest threat to abalone aquaculture production industries. Various measures have been taken to mitigate this issue by adjusting the environment; however, the cellular processes of Pacific abalone (Haliotis discus hannai) have been overlooked due to the paucity of genetic information. The draft genome of H. discus hannai has recently been reported, prompting exploration of the genes responsible for thermal regulation in Pacific abalone. In this study, 413 proteins were systematically annotated as members of the heat shock protein (HSP) super families, and among them 26 HSP genes from four Pacific abalone tissues (hemocytes, gill, mantle, and muscle) were differentially expressed under cold and heat stress conditions. The co-expression network revealed that HSP expression patterns were tissue-specific and similar to those of other shellfish inhabiting intertidal zones. Finally, representative HSPs were selected at random and their expression patterns were identified by RNA sequencing and validated by qRT-PCR to assess expression significance. The HSPs expressed in hemocytes were highly similar in both analyses, suggesting that hemocytes could be more reliable samples for validating thermal condition markers compared to other tissues.
Collapse
|
42
|
Im J, Kim HS. Genetic features of Haliotis discus hannai by infection of vibrio and virus. Genes Genomics 2019; 42:117-125. [PMID: 31776802 DOI: 10.1007/s13258-019-00892-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Haliotis discus hannai more commonly referred to as the Pacific Abalone is of significant commercial and economical value in South Korea, with it being the second largest producer in the world. Despite this significance there is a lack of genetic studies with regards to the species. Most existing studies focused mainly on environmental factors. OBJECTIVE To provide a comprehensive review describing the genetic feature of Haliotis discus hannai by infection of vibrio and virus. METHODS This review summarized the immune response in the Haliotis spp. with regards to immunological genes such as Cathepsin B, C-type lectin and Toll-like receptors. Genetic studies with regards to transposable elements and miRNAs are few and far between. A study identified LTR retrotransposon Ty3/gypsy in the species. As to miRNA, a single study identified numerous miRNAs in the Haliotis discus hannai. CONCLUSION This paper sought to provide an overview of genetic perspective with regards to immune response genes, transposable elements and miRNAs.
Collapse
Affiliation(s)
- Jennifer Im
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea. .,Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
| |
Collapse
|
43
|
Greenlip Abalone ( Haliotis laevigata) Genome and Protein Analysis Provides Insights into Maturation and Spawning. G3-GENES GENOMES GENETICS 2019; 9:3067-3078. [PMID: 31413154 PMCID: PMC6778792 DOI: 10.1534/g3.119.400388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Wild abalone (Family Haliotidae) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian ‘greenlip’ abalone (Haliotis laevigata, Donovan 1808) and generated 11 tissue transcriptomes from a female adult abalone. Phylogenetic analysis of the greenlip abalone with reference to the Pacific abalone (Haliotis discus hannai) indicates that these abalone species diverged approximately 71 million years ago. This study presents an in-depth analysis into the features of reproductive dysfunction, where we provide the putative biochemical messenger components (neuropeptides) that may regulate reproduction including gonad maturation and spawning. Indeed, we isolate the egg-laying hormone neuropeptide and under trial conditions induce spawning at 80% efficiency. Altogether, we provide a solid platform for further studies aimed at stimulating advances in abalone aquaculture production. The H. laevigata genome and resources are made available to the public on the abalone ‘omics website, http://abalonedb.org.
Collapse
|
44
|
Song K, Wen S, Zhang G. Adaptive Evolution Patterns in the Pacific Oyster Crassostrea gigas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:614-622. [PMID: 31203476 DOI: 10.1007/s10126-019-09906-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
Estimation of adaptive evolution rates at the molecular level is important in evolutionary genomics. However, knowledge of adaptive evolutionary patterns in Mollusca is very scarce, especially for oysters. Such information would help clarify how oysters adapt to pathogen-rich and dynamically changing intertidal environments. In this study, we characterized the patterns of adaptive evolution in the Crassostrea gigas genome, using population diversity analysis and congeneric comparison. Our analysis revealed that gene expression patterns were positively associated with adaptive evolution rates, which suggested that positive selection played an important role in gene evolution. The genes with more exons and alternative splicing events had higher adaptive evolution rates. The rates of adaptive evolution in immune-related and stress-response genes were higher than those in other genes, suggesting that these groups of genes experienced strong positive selection. This study represents the first analysis of adaptive evolution rates in oysters and the first comprehensive study of a Mollusca species. These results provide a system-level investigation of association between adaptive evolution rates with some intrinsic genetic factors. They also suggest that adaptation to pathogens and environmental stressors are important forces driving the adaptive evolution of genes.
Collapse
Affiliation(s)
- Kai Song
- School of Mathematics and Statistics, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Shiyong Wen
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot, 010018, China
- Dezhou State-owned Assets Supervision and Administration Commission, Dezhou,, 253000, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.
| |
Collapse
|
45
|
Gan HM, Tan MH, Austin CM, Sherman CDH, Wong YT, Strugnell J, Gervis M, McPherson L, Miller AD. Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone ( Haliotis rubra). Front Genet 2019; 10:889. [PMID: 31608118 PMCID: PMC6774278 DOI: 10.3389/fgene.2019.00889] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/23/2019] [Indexed: 01/05/2023] Open
Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Mun Hua Tan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M. Austin
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Craig D. H. Sherman
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Yen Ting Wong
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Jan Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Mark Gervis
- Southern Ocean Mariculture, Port Fairy, VIC, Australia
| | | | - Adam D. Miller
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| |
Collapse
|
46
|
Neave MJ, Corbeil S, McColl KA, Crane MSJ. Investigating the natural resistance of blackfoot p-a%%KERN_ERR%%ua Haliotis iris to abalone viral ganglioneuritis using whole transcriptome analysis. DISEASES OF AQUATIC ORGANISMS 2019; 135:107-119. [PMID: 31342912 DOI: 10.3354/dao03390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The natural resistance of New Zealand blackfoot p-a%%%%%%%%%%%%%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%KERN_ERR%%ua Haliotis iris to infection by haliotid herpesvirus-1 (HaHV-1) and to the disease abalone viral ganglioneuritis was investigated in experimentally challenged p-aua using high throughput RNA-sequencing. HaHV-1-challenged p-aua up-regulated broad classes of genes that contained chitin-binding peritrophin-A domains, which seem to play diverse roles in the p-aua immune response. The p-aua also up-regulated vascular adhesion protein-1 (VAP-1), an important adhesion molecule for lymphocytes, and chitotriosidase-1 (CHIT-1), an immunologically important gene in mammalian immune systems. Moreover, several blood coagulation pathways were dysregulated in the p-aua, possibly indicating viral modulation. We also saw several indications that neurological tissues were specifically affected by HaHV-1, including the dysregulation of beta-1,4-N-acetylgalactosaminyltransferase (B4GALNT), GM2 ganglioside, neuroligin-4 and the Notch signalling pathway. This research may support the development of molecular therapeutics useful to control and/or manage viral outbreaks in abalone culture.
Collapse
Affiliation(s)
- Matthew J Neave
- Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220, Australia
| | | | | | | |
Collapse
|
47
|
Kang HY, Lee YJ, Song WY, Kim TI, Lee WC, Kim TY, Kang CK. Physiological responses of the abalone Haliotis discus hannai to daily and seasonal temperature variations. Sci Rep 2019; 9:8019. [PMID: 31142794 PMCID: PMC6541628 DOI: 10.1038/s41598-019-44526-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/17/2019] [Indexed: 01/07/2023] Open
Abstract
Organisms inhabiting tidal mixing-front zones in shallow temperate seas are subjected to large semidiurnal temperature fluctuations in summer. The ability to optimize energy acquisition to this episodic thermal oscillation may determine the survival, growth and development of these ectotherms. We compared the physiological and molecular responses of Haliotis discus hannai cultivated in suspended cages to fluctuating or stable temperature conditions. Several physiological indicators (respiration, excretion rates and O:N) were measured in both conditions, and alterations in the proteome during thermal fluctuations were assessed. No summer mortality was observed in abalone cultivated in fluctuating temperatures compared with that at stable high temperatures. Metabolic rates increased sharply during stable warm summer conditions and fluctuated in accordance with short-term temperature fluctuations (20–26 °C). Ammonia excretion rates during acute responses were comparable in both conditions. When abalone were exposed to fluctuating temperatures, enzyme activities were downregulated and structure-related protein expression was upregulated compared with that at an acclimation temperature (26 °C), highlighting that exposure to low temperatures during fluctuations alters molecular processes. Our results reveal that modulation of physiological traits and protein expression during semidiurnal thermal fluctuations may buffer abalone from the lethal consequences of extreme temperatures in summer.
Collapse
Affiliation(s)
- Hee Yoon Kang
- Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering, Gwangju, 61005, Republic of Korea
| | - Young-Jae Lee
- Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering, Gwangju, 61005, Republic of Korea
| | - Woo-Young Song
- Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering, Gwangju, 61005, Republic of Korea
| | - Tae-Ik Kim
- National Institute of Fisheries Science, Southwest Sea Fisheries Research Institute, Gyeongnam, 53085, Republic of Korea
| | - Won-Chan Lee
- National Institute of Fisheries Science, Marine Environment Research Division, Busan, 46083, Republic of Korea
| | - Tae Young Kim
- Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering, Gwangju, 61005, Republic of Korea.
| | - Chang-Keun Kang
- Gwangju Institute of Science and Technology, School of Earth Sciences and Environmental Engineering, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
48
|
Dual Transcriptomic Analysis Reveals a Delayed Antiviral Response of Haliotis diversicolor supertexta against Haliotid Herpesvirus-1. Viruses 2019; 11:v11040383. [PMID: 31022987 PMCID: PMC6520846 DOI: 10.3390/v11040383] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022] Open
Abstract
Haliotid herpesvirus-1 (HaHV-1) is the first identified gastropod herpesvirus, causing a highly lethal neurologic disease of abalone species. The genome of HaHV-1 has been sequenced, but the functions of the putative genes and their roles during infection are still poorly understood. In the present study, transcriptomic profiles of Haliotis diversicolor supertexta at 0, 24 and 60 h post injection (hpi) with HaHV-1 were characterized through high-throughput RNA sequencing. A total of 448 M raw reads were obtained and assembled into 2.08 × 105 unigenes with a mean length of 1486 bp and an N50 of 2455 bp. Although we detected increased HaHV-1 DNA loads and active viral expression at 24 hpi, this evidence was not linked to significant changes of host transcriptomic profiles between 0 and 24 hpi, whereas a rich immune-related gene set was over-expressed at 60 hpi. These results indicate that, at least at the beginning of HaHV-1 infection, the virus can replicate with no activation of the host immune response. We propose that HaHV-1 may evolve more effective strategies to modulate the host immune response and hide during replication, so that it could evade the immune surveillance at the early stage of infection.
Collapse
|
49
|
Kim MA, Markkandan K, Han NY, Park JM, Lee JS, Lee H, Sohn YC. Neural Ganglia Transcriptome and Peptidome Associated with Sexual Maturation in Female Pacific Abalone ( Haliotis discus hannai). Genes (Basel) 2019; 10:genes10040268. [PMID: 30987054 PMCID: PMC6523705 DOI: 10.3390/genes10040268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/13/2019] [Accepted: 03/29/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic information of reproduction and growth is essential for sustainable molluscan fisheries and aquaculture management. However, there is limited knowledge regarding the reproductive activity of the commercially important Pacific abalone Haliotisdiscushannai. We performed de novo transcriptome sequencing of the ganglia in sexually immature and mature female Pacific abalone to better understand the sexual maturation process and the underlying molecular mechanisms. Of the ~305 million high-quality clean reads, 76,684 transcripts were de novo-assembled with an average length of 741 bp, 28.54% of which were annotated and classified according to Gene Ontology terms. There were 256 differentially expressed genes between the immature and mature abalone. Tandem mass spectrometry analysis, as compared to the predicted-peptide database of abalone ganglia transcriptome unigenes, identified 42 neuropeptide precursors, including 29 validated by peptidomic analyses. Label-free quantification revealed differential occurrences of 18 neuropeptide families between immature and mature abalone, including achatin, FMRFamide, crustacean cardioactive peptide, and pedal peptide A and B that were significantly more frequent at the mature stage. These results represent the first significant contribution to both maturation-related transcriptomic and peptidomic resources of the Pacific abalone ganglia and provide insight into the roles of various neuropeptides in reproductive regulation in marine gastropods.
Collapse
Affiliation(s)
- Mi Ae Kim
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung 25457, Korea.
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung 25457, Korea.
| | | | - Na-Young Han
- College of Pharmacy, Gachon University, Incheon 21936, Korea.
| | - Jong-Moon Park
- College of Pharmacy, Gachon University, Incheon 21936, Korea.
| | - Jung Sick Lee
- Department of Aqualife Medicine, Chonnam National University, Yeosu 59626, Korea.
| | - Hookeun Lee
- College of Pharmacy, Gachon University, Incheon 21936, Korea.
| | - Young Chang Sohn
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung 25457, Korea.
| |
Collapse
|
50
|
Cai H, Li Q, Fang X, Li J, Curtis NE, Altenburger A, Shibata T, Feng M, Maeda T, Schwartz JA, Shigenobu S, Lundholm N, Nishiyama T, Yang H, Hasebe M, Li S, Pierce SK, Wang J. A draft genome assembly of the solar-powered sea slug Elysia chlorotica. Sci Data 2019; 6:190022. [PMID: 30778257 PMCID: PMC6380222 DOI: 10.1038/sdata.2019.22] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/10/2019] [Indexed: 11/09/2022] Open
Abstract
Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is well-known for its ability to sequester chloroplasts from its algal prey and survive by photosynthesis for up to 12 months in the absence of food supply. Here we present a draft genome assembly of E. chlorotica that was generated using a hybrid assembly strategy with Illumina short reads and PacBio long reads. The genome assembly comprised 9,989 scaffolds, with a total length of 557 Mb and a scaffold N50 of 442 kb. BUSCO assessment indicated that 93.3% of the expected metazoan genes were completely present in the genome assembly. Annotation of the E. chlorotica genome assembly identified 176 Mb (32.6%) of repetitive sequences and a total of 24,980 protein-coding genes. We anticipate that the annotated draft genome assembly of the E. chlorotica sea slug will promote the investigation of sacoglossan genetics, evolution, and particularly, the genetic signatures accounting for the long-term functioning of algal chloroplasts in an animal.
Collapse
Affiliation(s)
- Huimin Cai
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | | | - Ji Li
- BGI-Shenzhen, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Nicholas E Curtis
- Department of Biology, Ave Maria University, Ave Maria, Florida 34142, USA
| | - Andreas Altenburger
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Tomoko Shibata
- National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Mingji Feng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Taro Maeda
- National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Julie A Schwartz
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Nina Lundholm
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, Okazaki 444-8585, Japan.,Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Sidney K Pierce
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA.,Department of Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| |
Collapse
|