1
|
Li F, Chen S, Zhang T, Pan L, Liu C, Bian L. Gonadal Transcriptome Sequencing Analysis Reveals the Candidate Sex-Related Genes and Signaling Pathways in the East Asian Common Octopus, Octopus sinensis. Genes (Basel) 2024; 15:682. [PMID: 38927618 PMCID: PMC11202624 DOI: 10.3390/genes15060682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The East Asian common octopus (Octopus sinensis) is an economically important species among cephalopods. This species exhibits a strict dioecious and allogamous reproductive strategy, along with a phenotypic sexual dimorphism, where the third right arm differentiates into hectocotylus in males. However, our understanding of the molecular mechanisms that underlie sex determination and differentiation in this species remains limited. In the present study, we surveyed gene-expression profiles in the immature male and female gonads of O. sinensis based on the RNA-seq, and a total of 47.83 Gb of high-quality data were generated. Compared with the testis, we identified 8302 differentially expressed genes (DEGs) in the ovary, of which 4459 genes were up-regulated and 3843 genes were down-regulated. Based on the GO enrichment, many GO terms related to sex differentiation were identified, such as sex differentiation (GO: 0007548), sexual reproduction (GO: 0019953) and male sex differentiation (GO: 0046661). A KEGG classification analysis identified three conserved signaling pathways that related to sex differentiation, including the Wnt signaling pathway, TGF-β signaling pathway and Notch signaling pathway. Additionally, 21 sex-related DEGs were selected, of which 13 DEGs were male-biased, including Dmrt1, Foxn5, Foxj1, Sox30, etc., and 8 DEGs were female-biased, including Sox14, Nanos3, β-tubulin, Suh, etc. Ten DEGs were used to verify the expression patterns in the testis and ovary using the RT-qPCR method, and the results showed that the expression level shown by RT-qPCR was consistent with that from the RNA-seq, which confirmed the reliability of the transcriptome data. The results presented in this study will not only contribute to our understanding of sex-formation mechanisms in O. sinensis but also provide the foundational information for further investigating the molecular mechanisms that underline its gonadal development and facilitate the sustainable development of octopus artificial breeding.
Collapse
Affiliation(s)
- Fenghui Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Siqing Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Zhang
- Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China;
| | - Luying Pan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Changlin Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Li Bian
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (F.L.); (S.C.); (L.P.); (C.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| |
Collapse
|
2
|
Li F, Kong N, Zhao J, Zhao B, Liu J, Yang C, Wang L, Song L. The intestinal bacterial community over seasons and its relationship with physiological status of Yesso scallop Patinopecten yessoensis. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109030. [PMID: 37634756 DOI: 10.1016/j.fsi.2023.109030] [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: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Emerging evidence indicates that the intestinal bacterial communities associated with eukaryotes play critical roles in the physiological activities and health of their hosts. Yesso scallop Patinopecten yessoensis, one of the cold-water aquaculture species in the North Yellow Sea of China, has suffered from massive mortality in recent years. In the present study, P. yessoensis were collected from Zhangzi Island, Dalian from March 2021 to January 2022 to investigate the intestinal bacterial community and physiological indices. 16S rRNA gene sequencing data revealed that the diversity of intestinal bacteria changed significantly over seasons, with the highest Chao1 (237.42) and Shannon (6.13) indices detected in January and the lowest Chao1 (115.44) and Shannon (2.73) indices detected in July. Tenericutes, Proteobacteria and Firmicutes were dominant phyla in the intestinal bacteria of P. yessoensis, among which Firmicutes and Proteobacteria significantly enriched in August and January, respectively. Mycoplasma was the most abundant genus during the sampling period, which exhibited the highest abundance in October (75.26%) and lowest abundance in August (13.15%). The functional profiles of intestinal bacteria also exhibited seasonal variation, with the pathways related to pentose phosphate and deoxyribonucleotides biosynthesis enriched in August while the glycogen biosynthesis pathway enriched in October. Redundancy analysis showed that seawater pH, dissolved inorganic nitrogen and silicate were major environmental factors driving the temporal succession of scallop intestinal bacteria. Correlation clustering analysis suggested that the relative abundances of Endozoicomonas and Vibrio in the intestine were positively correlated with superoxide dismutase activity in hepatopancreas while negatively correlated with malondialdehyde content in hepatopancreas and glycogen content in adductor muscle. All the results revealed that the intestine harbored a lower bacterial diversity and a higher abundance of Vibrio in August, compared to January, which were closely related to the oxidative stress status of scallop in summer. These findings will advance our understanding of the relationship between seasonal alteration in the intestinal bacteria and the physiological status of scallops.
Collapse
Affiliation(s)
- Fuzhe Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Ning Kong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Junyan Zhao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Bao Zhao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Jinyu Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chuanyan Yang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| |
Collapse
|
3
|
Patnaik HH, Sang MK, Park JE, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Patnaik BB, Lee YS. A review of the endangered mollusks transcriptome under the threatened species initiative of Korea. Genes Genomics 2023; 45:969-987. [PMID: 37405596 DOI: 10.1007/s13258-023-01389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/09/2023] [Indexed: 07/06/2023]
Abstract
Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea's protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research.
Collapse
Affiliation(s)
- Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, 37242, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, 56212, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, Chungnam, 31539, South Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- P.G Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, 756089, Nuapadhi, Balasore, India
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea.
| |
Collapse
|
4
|
In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae. Genes (Basel) 2023; 14:genes14020332. [PMID: 36833259 PMCID: PMC9956114 DOI: 10.3390/genes14020332] [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: 12/04/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.
Collapse
|
5
|
Duan B, Mu S, Guan Y, Liu W, Kang T, Cheng Y, Li Z, Tian Y, Kang X. Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus). Front Genet 2022; 13:932173. [PMID: 35923702 PMCID: PMC9340201 DOI: 10.3389/fgene.2022.932173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise FST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.
Collapse
Affiliation(s)
- Baohua Duan
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yueqiang Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Weibiao Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Tongxu Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yana Cheng
- College of Life Sciences, Hebei University, Baoding, China
| | - Zejian Li
- Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, China
| | - Yang Tian
- Hebei Fishery Technology Extension Station, Shijiazhuang, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
- Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
- *Correspondence: Xianjiang Kang,
| |
Collapse
|
6
|
Liu A, Hou X, Zhang J, Wang W, Dong X, Li J, Zhu X, Xing Q, Huang X, Hu J, Bao Z. Tissue-Specific and Time-Dependent Expressions of PC4s in Bay Scallop ( Argopecten irradians irradians) Reveal Function Allocation in Thermal Response. Genes (Basel) 2022; 13:genes13061057. [PMID: 35741819 PMCID: PMC9223095 DOI: 10.3390/genes13061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/10/2022] Open
Abstract
Transcriptional coactivator p15 (PC4) encodes a structurally conserved but functionally diverse protein that plays crucial roles in RNAP-II-mediated transcription, DNA replication and damage repair. Although structures and functions of PC4 have been reported in most vertebrates and some invertebrates, the PC4 genes were less systematically identified and characterized in the bay scallop Argopecten irradians irradians. In this study, five PC4 genes (AiPC4s) were successfully identified in bay scallops via whole-genome scanning through in silico analysis. Protein structure and phylogenetic analyses of AiPC4s were conducted to determine the identities and evolutionary relationships of these genes. Expression levels of AiPC4s were assessed in embryos/larvae at all developmental stages, in healthy adult tissues and in different tissues (mantles, gills, hemocytes and hearts) being processed under 32 °C stress with different time durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d and 10 d). Spatiotemporal expression profiles of AiPC4s suggested the functional roles of the genes in embryos/larvae at all developmental stages and in healthy adult tissues in bay scallop. Expression regulations (up- and down-) of AiPC4s under high-temperature stress displayed both tissue-specific and time-dependent patterns with function allocations, revealing that AiPC4s performed differentiated functions in response to thermal stress. This work provides clues of molecular function allocation of PC4 in scallops in response to thermal stress and helps in illustrating how marine bivalves resist elevated seawater temperature.
Collapse
Affiliation(s)
- Ancheng Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Wen Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xuecheng Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Jianshu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: ; Tel.: +86-532-82031969
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Yushan Campus, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (A.L.); (X.H.); (J.Z.); (W.W.); (X.D.); (J.L.); (X.Z.); (X.H.); (J.H.); (Z.B.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
7
|
Molecular allocation of PC4s provides implications for deciphering thermal response in Zhikong scallop (Chlamys farreri). Gene 2022; 818:146216. [PMID: 35093447 DOI: 10.1016/j.gene.2022.146216] [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: 07/26/2021] [Revised: 10/04/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022]
Abstract
The increasing sea temperature caused by global warming has led to serious death of Zhikong scallop (Chlamys farreri) and improving its thermal tolerance has become an active research area in scallop aquaculture industry. Gene transcriptional coactivator p15 (PC4) plays pivotally multi-faced roles in most vertebrates and some invertebrates, but the systematic identification and characterization of PC4 genes have less been reported in scallops. In this study, 15 PC4 genes (CfPC4s) were identified in Zhikong scallop through whole-genome scanning, including two pairs of tandem duplicate genes located in the same scaffold (CF-19495.9 and CF-19495.10, CF-6819.1 and CF-6819.2). Protein structural and phylogenetic analyses were performed to verify identities and evolutionary relationships of these genes. Spatiotemporal expression patterns were determined at different development stages and in healthy adult tissues, as well as expression regulations in selected tissues (mantles, gills, hemocytes and hearts) after high temperatures challenge (27 °C) with different durations (3 h, 6 h, 12 h, 24 h, 3 d, 6 d, 15 d and 30 d). Spatiotemporal expressions of CfPC4s were ubiquitous but exhibited different patterns, suggesting the functional roles of CfPC4s in all stages of growth and development of the scallop. Expression regulations of CfPC4s and their functional related factors (TFIIA, TFIID, TFIIH and RNAPII) in pre-initiation complex (PIC) in various tissues displayed up- and/or down-regulated responses at different time points, showing time- and/or tissue-dependent expression patterns with function allocation upon different thermal durations. Collectively, this study demonstrated that gene allocation of CfPC4s provided implications for deciphering thermal response in Zhikong scallop and potentially helped in developing strategies for long-term healthy sustainable Zhikong scallop culture.
Collapse
|
8
|
Metabolic Pathways Involved in the Drought Stress Response of Nitraria tangutorum as Revealed by Transcriptome Analysis. FORESTS 2022. [DOI: 10.3390/f13040509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drought resistance in plants is controlled by multiple genes. To identify the genes that mediate drought stress responses and to assess the associated metabolic pathways in the desert shrub Nitraria tangutorum, we conducted a transcriptome analysis of plants under control (maximum field capacity) and drought (20% of the maximum field capacity) conditions. We analyzed differentially expressed genes (DEGs) of N. tangutorum and their enrichment in the KEGG metabolic pathways database, and explored the molecular biological mechanisms underlying the answer to its drought tolerance. Between the control and drought groups, 119 classified metabolic pathways annotated 3047 DEGs in the KEGG database. For drought tolerance, nitrate reductase (NR) gene expression was downregulated, indicating that NR activity was decreased to improve drought tolerance. In ammonium assimilation, drought stress inhibited glutamine formation. Protochlorophyllide reductase (1.3.1.33) expression was upregulated to promote chlorophyll a synthesis, whereas divinyl reductase (1.3.1.75) expression was downregulated to inhibit chlorophyll-ester a synthesis. The expression of the chlorophyll synthase (2.5.1.62) gene was downregulated, which affected the synthesis of chlorophyll a and b. Overall, drought stress appeared to improve the ability to convert chlorophyll b into chlorophyll a. Our data serve as a theoretical foundation for further elucidating the growth regulatory mechanism of desert xerophytes, thereby facilitating the development and cultivation of new, drought-resistant genotypes for the purpose of improving desert ecosystems.
Collapse
|
9
|
Zeng Q, Hu B, Blanco AH, Zhang W, Zhao D, Martínez P, Hong Y. Full-Length Transcriptome Sequences Provide Insight Into Hermaphroditism of Freshwater Pearl Mussel Hyriopsis schlegelii. Front Genet 2022; 13:868742. [PMID: 35401664 PMCID: PMC8987123 DOI: 10.3389/fgene.2022.868742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
The freshwater mussel Hyriopsis schlegelii is a cultured bivalve in China, and the quality of the pearls produced is affected by the type of gonads. However, because of the lack of a published genome and the complexity of sex determination, research on sex reversal and development of this species is limited. In this study, Illumina RNA-seq and PacBio Isoform Sequencing (Iso-Seq) were combined to analyze the gonads of H. schlegelii. A total of 201,481 high-quality transcripts were generated. The study identified 7,922 differentially expressed genes in three comparison group (females versus males, hermaphrodites versus females, and hermaphrodites versus males). Twenty-four genes were identified as potential sex-related genes, including sox9 and wnt4 involved in sex determination, and vtg, cyp17a1 and 17β-hsd2 involved in gonadal development. We also speculated a possible pathways for the formation of hermaphroditism in H. schlegelii. The data provide a clear view of the transcriptome for H. schlegelii gonads and will be valuable in elucidating the mechanisms of gonad development.
Collapse
Affiliation(s)
- Qi Zeng
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Beijuan Hu
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
| | - Andres Hortas Blanco
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Wanchang Zhang
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Daxian Zhao
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
| | - Paulino Martínez
- Department of Zoology Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Yijiang Hong
- School of Life Sciences, Nanchang University, Nanchang, China
- Key Lab of Aquatic Resources and Utilization of Jiangxi, Nanchang, China
- Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang, China
- *Correspondence: Yijiang Hong,
| |
Collapse
|
10
|
Zhang J, Liao H, Xun X, Hou X, Zhu X, Xing Q, Huang X, Hu J, Bao Z. Identification, characterization and expression analyses of PC4 genes in Yesso scallop (Patinopecten yessoensis) reveal functional differentiations in response to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 244:106099. [PMID: 35114458 DOI: 10.1016/j.aquatox.2022.106099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/15/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Transcriptional coactivator p15 (PC4), considered a multifunctional chromosome associated protein, is actively involved in transcription regulation, DNA replication, damage repair and chromosome formation. Although studies have reported significant effects of PC4 in most vertebrates and some invertebrates, the complete PC4 gene members are less systematically identified and characterized in scallops. In this study, seven PC4 genes (PyPC4s) were identified in the Yesso scallop Patinopecten yessoensis using whole-genome scanning via bioinformatic analyses. Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of the seven genes. Expression profiles of PyPC4s were further investigated in embryos/larvae at all developmental stages, healthy adult tissues, and mantles that were exposed to low pH stress (pH 6.5 and 7.5) with different time durations (3, 6, 12 and 24 h). Spatiotemporal expression patterns indicated the functional roles of PyPC4s at all development stages and in healthy adult tissues, with PY-3235.33 demonstrating remarkably high constitutive expressions. Expression regulations (up- and down-regulation) of PyPC4s under low pH stress levels demonstrated a time-dependent pattern with functional complementation and/or enhancement, revealing that PyPC4s exhibited differentiated functions in response to ocean acidification (OA). Collectively, our data offer a novel perspective stating that low pH is a potential inducer leading to functional differentiation of PyPC4s in scallops. The results provide preliminary information on the versatile roles of PC4(s) in bivalves in response to OA.
Collapse
Affiliation(s)
- Junhao Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Qilu University of Technology (Shandong Academy of Sciences), China
| | - Xiujiang Hou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution of the Ocean University of China (SOI-OUC), Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
11
|
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
|
12
|
Effects of Ultrasound-Assisted Vacuum Impregnation Antifreeze Protein on the Water-Holding Capacity and Texture Properties of the Yesso Scallop Adductor Muscle during Freeze-Thaw Cycles. Foods 2022; 11:foods11030320. [PMID: 35159472 PMCID: PMC8834382 DOI: 10.3390/foods11030320] [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] [Received: 12/17/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/01/2023] Open
Abstract
The effect of antifreeze protein (AFP) on the water-holding capacity (WHC) and texture properties of the Patinopecten yessoensis adductor muscles during freeze–thaw cycles (FTCs) were evaluated based on three impregnation methods: general impregnation (GI), vacuum impregnation (VI), and ultrasound-assisted VI (US-VI). The WHC, texture properties, and tissue microstructure were all evaluated. Results showed that the WHC and texture properties of adductor muscle were significantly improved in the VI and US-VI groups during FTCs (p < 0.05). The WHC of the adductor muscle in the US-VI group was maximally enhanced in terms of yield (6.63%), centrifugal loss, cooking loss, and T22. The US-VI group of the adductor muscle had the optimal chewiness and springiness compared to others, and the shear force and hardness were most effectively enhanced by VI. The growth and recrystallization of ice crystals in the frozen adductor muscle were significantly inhibited by VI and US-VI. The average cross-sectional area and roundness of ice crystals in the US-VI group were decreased by 61.89% and increased by 22.22% compared with those of the control, respectively. The partial least squares regression (PLSR) model further confirmed that the WHC and texture properties of the adductor muscle were correlated appreciably with the degree of modification of ice crystal morphology through the AFP.
Collapse
|
13
|
Yuan C, Mao J, Sun H, Wang Y, Guo M, Wang X, Tian Y, Hao Z, Ding J, Chang Y. Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing. BMC Genomics 2021; 22:740. [PMID: 34649514 PMCID: PMC8515700 DOI: 10.1186/s12864-021-08055-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation. RESULTS In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop. CONCLUSIONS This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.
Collapse
Affiliation(s)
- Changzi Yuan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| | - Hongyan Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yiying Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ming Guo
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| |
Collapse
|
14
|
Li X, Li N, Zhao L, Shi J, Wang S, Ning X, Li Y, Hu X. Tissue distribution and seasonal accumulation of carotenoids in Yesso scallop (Mizuhopecten yessoensis) with orange adductor muscle. Food Chem 2021; 367:130701. [PMID: 34388635 DOI: 10.1016/j.foodchem.2021.130701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Carotenoids are colored compounds with important physiological functions. The Haida golden scallop, which has an orange adductor muscle, is a carotenoid-enriched variety of scallop Mizuhopecten yessoensis, an important aquaculture shellfish. In this study, we investigated the tissue distribution of the carotenoids, pectenolone and pectenoxanthin, in both Haida golden scallop and normal Yesso scallop. Both carotenoids were detected in all the sampled tissues of the two scallops, except in the adductor muscle of normal scallop. There were significantly more carotenoids in Haida golden scallop than in normal scallop, in the tissues of the mantle, female gonad, kidney, and adductor muscle. Increased carotenoid concentrations were detected in Haida golden scallop adductor muscle during the spring spawning season, indicating the effects of reproduction on muscle carotenoids accumulation. This study was the first systematic investigation of carotenoid distribution in Yesso scallop tissues and will benefit future research on carotenoid accumulation and function in scallops.
Collapse
Affiliation(s)
- Xue Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ning Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, Qingdao 266237, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shuyue Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xianhui Ning
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yueru Li
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, Qingdao 266237, China.
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, Qingdao 266237, China.
| |
Collapse
|
15
|
Fernández-González LE, Sánchez-Marín P, Gestal C, Beiras R, Diz AP. Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level. MARINE ENVIRONMENTAL RESEARCH 2021; 168:105315. [PMID: 33853012 DOI: 10.1016/j.marenvres.2021.105315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Vitellogenin (Vtg), a large multidomain protein precursor of egg-yolk proteins, is used as an endocrine disruption biomarker in fish, and in the last decades, its use has been extended to invertebrates like mollusks. However, it remains unclear whether invertebrate endocrine system produces Vtg in response to estrogens, like it occurs in oviparous vertebrates. In a previous study, no evidence of induction of Vtg expression at protein level was found in gonads of the marine mussel Mytilus galloprovincialis after exposure to the estrogenic chemical 17α-ethinylestradiol (EE2). In the present follow-up study, it was investigated whether there is any effect of EE2 on Vtg abundance at transcriptional level in M. galloprovincialis gonads. To this aim, RT-qPCR analysis targeting three different domains of Vtg transcript was performed on gonads of mussels that were exposed either 4 or 24 days to 100 ng/L EE2. In addition, several reference genes were analysed and a selection of these for potential use in further RT-qPCR analyses on mussel male and female gonads is provided. Results showed higher expression in females than in males for the three analysed Vtg domains, and no evidence of Vtg mRNA induction due to EE2 either in females or males. The present results, together with those obtained from previous analysis at protein level, support that Vtg is not an adequate biomarker for xenoestrogenicity in marine mussels. Additionally, nucleotide sequences of Vtg transcripts of three closely-related species from Mytilus edulis complex (M. galloprovincialis, M. edulis and M. trossulus) are provided and compared with Vtg sequences from other mollusk species to assess the level of conservation and evolutionary relationships among species.
Collapse
Affiliation(s)
- Laura Emilia Fernández-González
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Paula Sánchez-Marín
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, 36390, Vigo, Spain
| | - Camino Gestal
- Marine Molecular Pathobiology Group, Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Ricardo Beiras
- Department of Ecology and Animal Biology, University of Vigo, 36310, Vigo, Spain; Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain
| | - Angel P Diz
- Marine Research Centre, University of Vigo (CIM-UVIGO), Isla de Toralla, Vigo, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain.
| |
Collapse
|
16
|
Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing. Mol Biol Rep 2021; 48:4273-4283. [PMID: 34057686 DOI: 10.1007/s11033-021-06442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.
Collapse
|
17
|
Xing Q, Liao H, Peng C, Zheng G, Yang Z, Wang J, Lu W, Huang X, Bao Z. Identification, characterization and expression analyses of cholinesterases genes in Yesso scallop (Patinopecten yessoensis) reveal molecular function allocation in responses to ocean acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 231:105736. [PMID: 33422860 DOI: 10.1016/j.aquatox.2020.105736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Cholinesterases are key enzymes in central and peripheral cholinergic nerve system functioning on nerve impulse transmission in animals. Though cholinesterases have been identified in most vertebrates, the knowledge about the variable numbers and multiple functions of the genes is still quite meagre in invertebrates, especially in scallops. In this study, the complete cholinesterase (ChE) family members have been systematically characterized in Yesso scallop (Patinopecten yessoensis) via whole-genome scanning through in silico analysis. Ten ChE family members in the genome of Yesso scallop (designated PyChEs) were identified and potentially acted to be the largest number of ChE in the reported species to date. Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of these genes. The expression profiles of PyChEs were determined in all developmental stages, in healthy adult tissues, and in mantles under low pH stress (pH 6.5 and 7.5). Spatiotemporal expression suggested the ubiquitous functional roles of PyChEs in all stages of development, as well as general and tissue-specific functions in scallop tissues. Regulation expressions revealed diverse up- and down-regulated expression patterns at most time points, suggesting different functional specialization of gene superfamily members in response to ocean acidification (OA). Evidences in gene number, phylogenetic relationships and expression patterns of PyChEs revealed that functional innovations and differentiations after gene duplication may result in altered functional constraints among PyChEs gene clusters. Collectively, our results provide the potential clues that the selection pressures coming from the environment were the potential inducement leading to function allocation of ChE family members in scallop.
Collapse
Affiliation(s)
- Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Guiliang Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| |
Collapse
|
18
|
Rosen R, Lebedev G, Kontsedalov S, Ben-Yakir D, Ghanim M. A De Novo Transcriptomics Approach Reveals Genes Involved in Thrips Tabaci Resistance to Spinosad. INSECTS 2021; 12:67. [PMID: 33451167 PMCID: PMC7828677 DOI: 10.3390/insects12010067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/01/2021] [Accepted: 01/10/2021] [Indexed: 11/16/2022]
Abstract
The onion thrip, Thrips tabaci (Thysanoptera: Thripidae) is a major polyphagous pest that attacks a wide range of economically important crops, especially Allium species. The thrip's damage can result in yield loss of up to 60% in onions (Allium cepa). In the past few decades, thrip resistance to insecticides with various modes of actions have been documented. These include resistance to spinosad, a major active compound used against thrips, which was reported from Israel. Little is known about the molecular mechanisms underlying spinosad resistance in T. tabaci. We attempted to characterize the mechanisms involved in resistance to spinosad using quantitative transcriptomics. Susceptible (LC50 = 0.6 ppm) and resistant (LC50 = 23,258 ppm) thrip populations were collected from Israel. An additional resistant population (LC50 = 117 ppm) was selected in the laboratory from the susceptible population. De novo transcriptome analysis on the resistant and susceptible population was conducted to identify differently expressed genes (DGEs) that might be involved in the resistance against spinosad. In this analysis, 25,552 unigenes were sequenced, assembled, and functionally annotated, and more than 1500 DGEs were identified. The expression levels of candidate genes, which included cytochrome P450 and vittelogenin, were validated using quantitative RT-PCR. The cytochrome P450 expression gradually increased with the increase of the resistance. Higher expression levels of vitellogenin in the resistant populations were correlated with higher fecundity, suggesting a positive effect of the resistance on resistant populations. This research provides a novel genetic resource for onion thrips and a comprehensive molecular examination of resistant populations to spinosad. Those resources are important for future studies concerning thrips and resistance in insect pests regarding agriculture.
Collapse
Affiliation(s)
| | | | | | | | - Murad Ghanim
- Department of Entomology, Volcani Center, Rishon LeZion 7505101, Israel; (R.R.); (G.L.); (S.K.); (D.B.-Y.)
| |
Collapse
|
19
|
Li J, Zhou Y, Zhou Z, Lin C, Wei J, Qin Y, Xiang Z, Ma H, Zhang Y, Zhang Y, Yu Z. Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa). BMC Genomics 2020; 21:872. [PMID: 33287701 PMCID: PMC7720611 DOI: 10.1186/s12864-020-07276-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Gonad development and differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. However, the mechanisms underlying gonad development and gametogenesis remain unclear in Tridacna squamosa, a large-size bivalve of great ecological value. They are protandrous simultaneous hermaphrodites, with the male gonad maturing first, eventually followed by the female gonads. In this study, nine gonad libraries representing resting, male and hermaphrodite stages in T. squamosa were performed to identify the molecular mechanisms. RESULTS Sixteen thousand four hundred ninety-one unigenes were annotated in the NCBI non-redundant protein database. Among the annotated unigenes, 5091 and 7328 unigenes were assigned to Gene Ontology categories and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database, respectively. A total of 4763 differentially expressed genes (DEGs) were identified by comparing male to resting gonads, consisting of 3499 which were comparatively upregulated in males and 1264 which were downregulated in males. Six hundred-ninteen DEGs between male and hermaphroditic gonads were identified, with 518 DEGs more strongly expressed in hermaphrodites and 101 more strongly expressed in males. GO (Gene Ontology) and KEGG pathway analyses revealed that various biological functions and processes, including functions related to the endocrine system, oocyte meiosis, carbon metabolism, and the cell cycle, were involved in regulating gonadal development and gametogenesis in T. squamosa. Testis-specific serine/threonine kinases 1 (TSSK1), TSSK4, TSSK5, Doublesex- and mab-3-related transcription factor 1 (DMRT1), SOX, Sperm surface protein 17 (SP17) and other genes were involved in male gonadal development in Tridacna squamosal. Both spermatogenesis- (TSSK4, spermatogenesis-associated protein 17, spermatogenesis-associated protein 8, sperm motility kinase X, SP17) and oogenesis-related genes (zona pellucida protein, Forkhead Box L2, Vitellogenin, Vitellogenin receptor, 5-hydroxytryptamine, 5-hydroxytryptamine receptor) were simultaneously highly expressed in the hermaphroditic gonad to maintain the hermaphroditism of T. squamosa. CONCLUSION All these results from our study will facilitate better understanding of the molecular mechanisms underlying giant clam gonad development and gametogenesis, which can provided a base on obtaining excellent gametes during the seed production process for giant clams.
Collapse
Affiliation(s)
- Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yinyin Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zihua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxu Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jinkuan Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yanpin Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Science, 164 West Xingang Road, Guangzhou, 510301, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Sanya Institute of Oceanology Chinese Academy of Sciences, Sanya, 572024, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
20
|
Genome survey sequencing of Atractylodes lancea and identification of its SSR markers. Biosci Rep 2020; 40:226599. [PMID: 33026067 PMCID: PMC7593537 DOI: 10.1042/bsr20202709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/03/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022] Open
Abstract
Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine rich in sesquiterpenes that has been widely used in China and Japan for the treatment of viral infections. Despite its important pharmacological value, genomic information regarding A. lancea is currently unavailable. In the present study, the whole genome sequence of A. lancea was obtained using an Illumina sequencing platform. The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome. Based on the genomic data of A. lancea, 27,582 simple sequence repeat (SSR) markers were identified. The differences in representation among nucleotide repeat types were large, e.g., the mononucleotide repeat type was the most abundant (54.74%) while the pentanucleotide repeats were the least abundant (0.10%), and sequence motifs GA/TC (31.17%) and TTC/GAA (7.23%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. A total of 93,434 genes matched known genes in common databases including 48,493 genes in the Gene Ontology (GO) database and 34,929 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This is the first report to sequence and characterize the whole genome of A. lancea and will provide a theoretical basis and reference for further genome-wide deep sequencing and SSR molecular marker development of A. lancea.
Collapse
|
21
|
Genome-wide identification, characterisation and expression analysis of the ALAS gene in the Yesso scallop (Patinopecten yessoensis) with different shell colours. Gene 2020; 757:144925. [PMID: 32622991 DOI: 10.1016/j.gene.2020.144925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/13/2020] [Accepted: 06/27/2020] [Indexed: 12/19/2022]
Abstract
Porphyrins, one of the most common shell pigments, are by-products of the haem pathway. 5-Aminolaevulinate synthase (ALAS) is the first and rate-limiting enzyme in this pathway and has been well studied in vertebrate species. However, the function of ALAS in shell colouration has been poorly studied in molluscs, which are renowned for their colourful shells. In the present study, an ALAS gene, named PyALAS, was identified through whole-genome scanning in the Yesso scallop (Patinopecten yessoensis), an economically and evolutionarily important bivalve species in which the shell colour represents polymorphism. Two conserved domains were detected in the PyALAS protein sequence, including a Preseq-ALAS domain and a 5-ALAS domain, confirming the identification of PyALAS. Phylogenetic analysis of the ALAS proteins among various invertebrate and vertebrate species revealed a high consistency between the molecular evolution of ALAS and the species taxonomy. PyALAS was ubiquitously expressed in most adult tissues of the Yesso scallop. The left mantle expressed a significantly higher level of PyALAS than the right side in brown scallops, whereas there was no significant difference in white scallops. Significantly different expression levels of PyALAS was also detected between the two different shell colour strains. These data indicate that PyALAS plays an important role in shell colouration in Yesso scallops and the present study provides new insights into the molecular mechanism of shell colouration in molluscs.
Collapse
|
22
|
Bowen L, Counihan KL, Ballachey B, Coletti H, Hollmen T, Pister B, Wilson TL. Monitoring nearshore ecosystem health using Pacific razor clams (Siliqua patula) as an indicator species. PeerJ 2020; 8:e8761. [PMID: 32185117 PMCID: PMC7060925 DOI: 10.7717/peerj.8761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/17/2020] [Indexed: 12/05/2022] Open
Abstract
An emerging approach to ecosystem monitoring involves the use of physiological biomarker analyses in combination with gene transcription assays. For the first time, we employed these tools to evaluate the Pacific razor clam (Siliqua patula), which is important both economically and ecologically, as a bioindicator species in the northeast Pacific. Our objectives were to (1) develop biomarker and gene transcription assays with which to monitor the health of the Pacific razor clam, (2) acquire baseline biomarker and gene transcription reference ranges for razor clams, (3) assess the relationship between physiological and gene transcription assays and (4) determine if site-level differences were present. Pacific razor clams were collected in July 2015 and 2016 at three sites within each of two national parks in southcentral Alaska. In addition to determining reference ranges, we found differences in biomarker assay and gene transcription results between parks and sites which indicate variation in both large-scale and local environmental conditions. Our intent is to employ these methods to evaluate Pacific razor clams as a bioindicator of nearshore ecosystem health. Links between the results of the biomarker and gene transcription assays were observed that support the applicability of both assays in ecosystem monitoring. However, we recognize the need for controlled studies to examine the range of responses in physiology and gene transcripts to different stressors.
Collapse
Affiliation(s)
- Lizabeth Bowen
- Western Ecological Research Center, U.S. Geological Survey, Davis, CA, USA
| | | | - Brenda Ballachey
- Alaska Science Center, U.S. Geological Survey, Anchorage, AK, USA
| | - Heather Coletti
- Inventory & Monitoring Program, Southwest Alaska Network, National Park Service, Fairbanks, AK, USA
| | - Tuula Hollmen
- College of Fisheries and Ocean Sciences, Alaska SeaLife Center and University of Alaska Fairbanks, Seward, AK, USA
| | - Benjamin Pister
- Ocean Alaska Science and Learning Center, National Park Service, Seward, AK, USA
| | - Tammy L Wilson
- Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| |
Collapse
|
23
|
Zhu X, Liao H, Yang Z, Peng C, Lu W, Xing Q, Huang X, Hu J, Bao Z. Genome-wide identification, characterization of RLR genes in Yesso scallop (Patinopecten yessoensis) and functional regulations in responses to ocean acidification. FISH & SHELLFISH IMMUNOLOGY 2020; 98:488-498. [PMID: 31978530 DOI: 10.1016/j.fsi.2020.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/17/2020] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), are crucial sensors with a conserved structure in cytoplasm, inducing the production of cytokines, chemokines and host restriction factors which mediate a variety of intracellular activities to interfere with distinct PAMPs (pathogen-associated molecular patterns) for eliminating pathogens in innate immune system. Although RLR genes have been investigated in most vertebrates and some invertebrates, the systematic identification and characterization of RLR genes have not been reported in scallops. In this study, four RLR genes (PY-10413.4, PY-10413.5, PY-443.7 and PY-443.8, designated PyRLRs) were identified in Yesso scallop (Patinopecten yessoensis) through whole-genome scanning through in silico analysis, including two pairs of tandem duplicate genes located on the same scaffold (PY-10413.4 and PY-10413.5, PY-443.7 and PY-443.8, respectively). Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of these genes. The expression profiles of PyRLRs were determined in all developmental stages, in healthy adult tissues, and in mantles that simulated ocean acidification (OA) exposure (pH = 6.5 and 7.5) at different time points (3, 6, 12 and 24 h). Spatiotemporal expression patterns suggested the functional roles of PyRLRs in all stages of development and growth of the scallop. Regulation expressions revealed PY-10413.4 and PY-10413.5 with one or two CARD(s) (caspase activation and recruitment domain) were up-regulated expressed at most time points, whereas PY-443.8 and PY-10413.4 without CARD were significantly down-regulated at each time points, suggesting functional differentiations in the two pairs of PyRLRs based on the structural differences in response to OA. Collectively, this study demonstrated gene duplication of RLR family genes and provide primary analysis for versatile roles in the response of the bivalve innate immune system to OA challenge.
Collapse
Affiliation(s)
- Xinghai Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| |
Collapse
|
24
|
Sun Y, Zhang X, Wang Y, Day R, Yang H, Zhang Z. Immunity-related genes and signaling pathways under hypoxic stresses in Haliotis diversicolor: a transcriptome analysis. Sci Rep 2019; 9:19741. [PMID: 31874975 PMCID: PMC6930256 DOI: 10.1038/s41598-019-56150-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Due to increased temperatures and aquaculture density, thermal and hypoxia stresses have become serious problems for the aquaculture of abalone Haliotis diversicolor. Stresses lead to immunosuppression, which can cause severe negative impacts on aquaculture farms. To study the mechanism of immunosuppression after hypoxia stress and bacterial challenge, transcriptomes of H. diversicolor hemocytes involved in immunity were profiled. A total of 307,395,572 clean reads were generated and assembled into 99,774 unigenes. KEGG analysis indicated that 225 unigenes with immunologic function were mapped into immune-related pathways. Expression of 41 unigenes measured by quantitative real-time PCR (qRT-PCR) showed consistent results with that of transcriptome analysis. When exposure challenge of Vibrio parahaemolyticus, it is indicated that the PI3K-AKT, MAPK, NF-κB and P53 signal pathways were involved in the hypoxia-induced immunosuppression of H. diversicolor. Furthermore, when the AKT gene (HdAKT) was inhibited by double-stranded RNA (dsRNA), expression levels of HdAKT was lower than the blank and control group in hemocytes at 4 h, 12 h and 24 h (p < 0.05).
Collapse
Affiliation(s)
- Yulong Sun
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, P.R. China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, P.R. China
| | - Xin Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, P.R. China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, P.R. China
| | - Yilei Wang
- Fisheries College, Jimei University, Xiamen, 361021, China.
| | - Robert Day
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - 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, P.R. China.
- Fisheries College, Jimei University, Xiamen, 361021, China.
| |
Collapse
|
25
|
Yang Z, Li X, Liao H, Hu L, Peng C, Wang S, Huang X, Bao Z. A Molecular Cytogenetic Map of Scallop (Patinopecten yessoensis). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:731-742. [PMID: 31473865 DOI: 10.1007/s10126-019-09918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
To consolidate the genetic, physical, and cytogenetic maps of scallop (Patinopecten yessoensis), we constructed a molecular cytogenetic map by localizing 84 fosmid clones that contain different SNP markers from 19 linkage groups (LGs) using fluorescence in situ hybridization (FISH). Among these 84 SNP-anchored clones, 56 clones produced specific and stable signals on one pair of chromosomes. Dual-color FISH assigned 19 LGs to their corresponding chromosomes with 38 SNP-anchored clones as probes. Among these 19 LGs, 17 LGs were assigned to their corresponding one pair of chromosomes, while two clones containing SNPs from LG10 and LG19 were located on two different pairs of chromosomes separately. The orientation of 7 LGs was corrected according to the chromosome location of SNPs within the same LG. In addition, a probe panel of SNP-anchored clones was developed to identify each chromosome of P. yessoensis. The molecular cytogenetic map will facilitate molecular breeding in scallop and enable comparative studies on chromosome evolution of bivalve mollusk.
Collapse
Affiliation(s)
- Zujing Yang
- 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Yantai Fisheries Research Institute, Yantai, China
| | - Cheng Peng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shenhai Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- 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, 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
26
|
Mao J, Zhang W, Wang X, Song J, Yin D, Tian Y, Hao Z, Han B, Chang Y. Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:683-696. [PMID: 31385168 DOI: 10.1007/s10126-019-09913-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The molecular mechanisms of shell formation and pigmentation are issues of great interest in molluscan studies due to the unique physical and biological properties of shells. The Yesso scallop, Patinopecten yessoensis, is one of the most important maricultural bivalves in Asian countries, and its shell color shows polymorphism. To gain more information about the underlying mechanisms of shell formation and pigmentation, this study presents the first analyses of histological and transcriptional differences between different mantle regions of the Yesso scallop, which are thought to be responsible for the formation of different shell layers. The results showed major microstructural differences between the edge and central mantles, which were closely associated with their functions. Different biomineralization-related GO functions, which might participate in the formation of different shell layers, were significantly enriched in the different mantle regions, indicating the different molecular functions of the two mantle regions in shell formation. The melanogenesis pathway, which controls melanin biosynthesis, was the most significantly enriched pathway in the DEGs between the two mantle regions, indicating its important role in shell pigmentation. Tyr, the key and rate-limiting gene in melanogenesis, was expressed at a remarkably high level in the central mantle, while the upstream regulatory genes included in melanogenesis were mainly upregulated in the edge mantle, suggesting the different molecular functions of the two mantle regions in shell pigmentation.
Collapse
Affiliation(s)
- Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Wenjing Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Bing Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| |
Collapse
|
27
|
Yu Z, Liu C, Fu Q, Lu G, Han S, Wang L, Song L. The differences of bacterial communities in the tissues between healthy and diseased Yesso scallop (Patinopecten yessoensis). AMB Express 2019; 9:148. [PMID: 31522290 PMCID: PMC6745042 DOI: 10.1186/s13568-019-0870-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/30/2019] [Indexed: 02/02/2023] Open
Abstract
The tissues of marine invertebrates are colonized by species-rich microbial communities. The dysbiosis of host's microbiota is tightly associated with the invertebrate diseases. Yesso scallop (Patinopecten yessoensis), one of the most important maricultured scallops in northern China, has recently suffered massive summer mortalities, which causes huge production losses. The knowledge about the interactions between the Yesso scallop and its microbiota is important to develop the strategy for the disease prevention and control. In the present study, the bacterial communities in hemolymph, intestine, mantle and adductor muscle were compared between the healthy and diseased Yesso scallop based on the high-throughput sequencing of 16S rRNA gene. The results indicated obvious difference of the composition rather than the diversity of the bacterial communities between the healthy and diseased Yesso scallop. Vibrio, Francisella and Photobacterium were found to overgrow and dominate in the mantle, adductor muscle and intestine of the diseased scallops, respectively. The prediction of bacterial community metagenomes and the variations of KEGG pathways revealed that the proportions of the pathways related with neurodegenerative diseases and carbohydrate metabolism both increased significantly in the mantle and hemolymph of the diseased scallops. The abundance of the metabolism pathways including carbohydrate metabolism, lipid metabolism and amino acid metabolism decreased significantly in the intestine of diseased scallops. The results suggested that the changes of bacterial communities might be closely associated with the Yesso scallop's disease, which was helpful for further investigation of the pathogenesis as well as prevention and control of the disease in Yesso scallop.
Collapse
|
28
|
Zhang M, Li L, Liu Y, Gao X. Effects of a Sudden Drop in Salinity on Immune Response Mechanisms of Anadara kagoshimensis. Int J Mol Sci 2019; 20:ijms20184365. [PMID: 31491977 PMCID: PMC6769905 DOI: 10.3390/ijms20184365] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 11/16/2022] Open
Abstract
In this experiment, the effects of a sudden drop of salinity on the immune response mechanisms of the ark shell Anadara kagoshimensis were examined by simulating the sudden drop of salinity that occurs in seawater after a rainstorm. Additionally, the differentially expressed genes (DEGs) were identified using transcriptome sequencing. When the salinity dropped from 30‱ (S30) to 14‱ (S14), the phagocytic activity of blood lymphocytes, the O2- levels produced from respiratory burst, the content of reactive oxygen species, and the activities of lysozymes and acid phosphatases increased significantly, whereas the total count of blood lymphocytes did not increase. Total count of blood lymphocytes in 22‱ salinity (S22) was significantly higher than that in any other group. The raw data obtained from sequencing were processed with Trimmomatic (Version 0.36). The expression levels of unigenes were calculated using transcripts per million (TPM) based on the effects of sequencing depth, gene length, and sample on reads. Differential expression analysis was performed using DESeq (Version 1.12.4). Transcriptome sequencing revealed 269 (101 up-regulated, 168 down-regulated), 326 (246 up-regulated, 80 down-regulated), and 185 (132 up-regulated, 53 down-regulated) significant DEGs from comparison of the S14 vs. S22, S22 vs. S30, and S14 vs. S30 groups, respectively. Gene Ontology enrichment analysis of the DEGs in these salinity comparison groups revealed that the cellular amino acid metabolic process, the regulation of protein processing, the regulation of response to stress, and other terms were significantly enriched. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that nucleotide-binding, oligomerization domain (NOD)-like receptor signaling pathway (ko04621), apoptosis-multiple species (ko04215), Toll and Imd signaling pathway (ko04624), NF-κB signaling pathway (ko04064), apoptosis (ko04210), and focal adhesion (ko04510) were significantly enriched in all salinity comparison groups. qRT-PCR verification of 12 DEGs in the above six pathways was conducted, and the results were consistent with the transcriptome sequencing results in terms of up-regulation and down-regulation, which illustrates that the transcriptome sequencing data are credible. These results were used to preliminarily explore the effects of a sudden drop of salinity on blood physiological and biochemical indexes and immunoregulatory mechanisms of A. kagoshimensis. They also provide a theoretical basis for the selection of bottom areas optimal for release and proliferation of A. kagoshimensis required to restore the declining populations of this species.
Collapse
Affiliation(s)
- Mo Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Li Li
- Marine Biology Institute of Shandong Province, Qingdao 266104, China.
| | - Ying Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
| | - Xiaolong Gao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
29
|
Zhou L, Liu Z, Dong Y, Sun X, Wu B, Yu T, Zheng Y, Yang A, Zhao Q, Zhao D. Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis). BMC Genomics 2019; 20:671. [PMID: 31443640 PMCID: PMC6708199 DOI: 10.1186/s12864-019-6021-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Background The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. Results In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1, which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway. Conclusions The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis. Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function. Electronic supplementary material The online version of this article (10.1186/s12864-019-6021-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Liqing Zhou
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhihong Liu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Xiujun Sun
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Biao Wu
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tao Yu
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Yanxin Zheng
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Science, Changdao, China
| | - Aiguo Yang
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China. .,Labortory for Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qing Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Dan Zhao
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Qingdao, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
30
|
Fu S, Lei M, Zhang Y, Deng Z, Shi J, Hao D. De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana. Genet Mol Biol 2019; 42:480-487. [PMID: 31259355 PMCID: PMC6726160 DOI: 10.1590/1678-4685-gmb-2018-0033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 10/16/2018] [Indexed: 11/21/2022] Open
Abstract
Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes were identified as differentially expressed between flowers and leaves, and used in further enrichment analysis. Also, 2,156 unigenes were annotated as transcription factors. Furthermore, our transcriptome analysis resulted in the identification of candidate unigenes annotated to enzymes involved in terpenoid biosynthesis. Taken together, this work has laid the foundation for the investigation of secondary metabolite biosynthesis and other physiological processes of D. schraderiana.
Collapse
Affiliation(s)
- Suhong Fu
- Molecular Medical Laboratory, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Ming Lei
- School of Science, Tibet University, Lhasa, China
| | - Yongqun Zhang
- Molecular Medical Laboratory, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Zhaomin Deng
- Molecular Medical Laboratory, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Jing Shi
- Molecular Medical Laboratory, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| | - Doudou Hao
- Molecular Medical Laboratory, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu, China
| |
Collapse
|
31
|
Phenotypic Stability of Sex and Expression of Sex Identification Markers in the Adult Yesso Scallop Mizuhopecten yessoensis throughout the Reproductive Cycle. Animals (Basel) 2019; 9:ani9050277. [PMID: 31137722 PMCID: PMC6562885 DOI: 10.3390/ani9050277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023] Open
Abstract
Simple Summary Bivalve sex is thought to fluctuate depending on environmental conditions. So far, there has been no investigation on the phenotypic stability of sex in the commercially important Yesso scallop Mizuhopecten yessoensis. The present study revealed that the sex of the Yesso scallop is stable after initial sex differentiation and that this species maintains a sex-stable maturation system throughout its life. In addition, gonad differentiation for each sex was precisely characterized by using molecular markers throughout the maturational cycle. Abstract The objective of the present study was to analyze the phenotypic stability of sex after sex differentiation in the Yesso scallop, which is a gonochoristic species that has been described as protandrous. So far, no study has investigated in detail the sexual fate of the scallop after completion of sex differentiation, although bivalve species often show annual sex change. In the present study, we performed a tracking experiment to analyze the phenotypic stability of sex in scallops between one and two years of age. We also conducted molecular marker analyses to describe sex differentiation and gonad development. The results of the tracking experiment revealed that all scallops maintained their initial sex phenotype, as identified in the last reproductive period. Using molecular analyses, we characterized my-dmrt2 and my-foxl2 as sex identification markers for the testis and ovary, respectively. We conclude by proposing that the Yesso scallop is a sex-stable bivalve after its initial sex differentiation and that it maintains a sex-stable maturation system throughout its life. The sex-specific molecular markers identified in this study are useful tools to assess the reproductive status of the Yesso scallop.
Collapse
|
32
|
Zhu X, Wang J, Lv J, Liu P, Zhang L, Jiao W, Ma C, Bao Z, Wang S. Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies. Evol Bioinform Online 2019; 15:1176934319836074. [PMID: 30886517 PMCID: PMC6413421 DOI: 10.1177/1176934319836074] [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: 02/01/2019] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Transcriptome-wide targeted genotyping is highly attractive for
evolutionary and ecological studies but, until recently, accomplishing
this goal presented a major technical barrier for the study of
non-model organisms. Our group has recently developed a
high-throughput targeted genotyping approach (called HD-Marker) based
on the high specificity and accuracy of oligo extension-ligation
assays that facilitates the design of assays tailored to meet specific
genotyping needs. HD-Marker allows for targeted genotyping of over 10
000 genes in a single tube, with strikingly high capture rate
(98%-99%) and genotyping accuracy (97%-99%). With the remarkable
advantages of cost-effectiveness and flexibility, we envision that
HD-Marker has broad application potential in evolutionary and
ecological studies.
Collapse
Affiliation(s)
- Xuan Zhu
- 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jia Lv
- 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Cen Ma
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 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, 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, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
33
|
Wei Z, Liu X, Zhou Z, Xu J. De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids. Genes Genomics 2019; 41:583-597. [PMID: 30830682 DOI: 10.1007/s13258-019-00799-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Strongylocentrotus nudus is an important cultured sea urchin species in north China, because its gonad is rich in unsaturated fatty acids, particularly long polyunsaturated fatty acids (LC-PUFAs). These PUFAs play pleiotropic and crucial roles in a wide range of biological process. OBJECTIVE However, the genes contributing to biosynthesis PUFAs have not been elucidated yet, and the molecular mechanism relative to the difference in PUFA composition between male and female gonad as been revealed but the corresponding has not been understood. METHODS In this paper, solexa sequencing based transcriptomic approach was used to identify and characterize the key genes relative to PUFA synthesis and further conducted different expressed genes between male and female gonad. RESULTS A total of 130,124 transcripts and 189330 unigenes were de novo assembled from 64.32 Gb data. Next, these unigenes were subjected to functional annotation by mapping to six public databases, and this process revealed a lot of genes involving in lipid metabolism. In addition, three types of fatty acids front-end desaturase and three species of very long fatty acids elongase were identified and the pathway for PUFA biosynthesis was hypothesized. Last, comparative analysis revealed the higher expression level of Δ5 desaturase, Δ6 desaturase, ELOVL-4, -6 and -7 in male gonad compared with female. CONCLUSION This results could plausible explain the differ in composition of PUFAs between male and female gonad of sea urchin.
Collapse
Affiliation(s)
- Zhenlin Wei
- Biological Sciences Department, Dezhou University, Dezhou, 253023, Shandong, China.
| | - Xiaolin Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, Liaoning, China
| | - Junxiao Xu
- Biological Sciences Department, Dezhou University, Dezhou, 253023, Shandong, China
| |
Collapse
|
34
|
Thitiphuree T, Nagasawa K, Osada M. Molecular identification of steroidogenesis-related genes in scallops and their potential roles in gametogenesis. J Steroid Biochem Mol Biol 2019; 186:22-33. [PMID: 30195968 DOI: 10.1016/j.jsbmb.2018.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/09/2023]
Abstract
Sex steroids are crucial for controlling gametogenesis and germ cell maturation in vertebrates. It has been proposed that Yesso scallop (Mizuhopecten yessoensis) has the same sex steroids as those animals, but the scallop biosynthetic pathway is unclear. In this study, we characterized several steroidogenesis-related genes in M. yessoensis and proposed a putative biosynthetic pathway for sex steroids that is similar to that of vertebrates. Specifically, we identified several steroidogenesis-related gene sequences that encode steroid metabolizing enzymes: StAR-related lipid transfer (START) protein, 17α-hydroxylase, 17,20-lyase (cyp17a), 17β-hydroxysteroid dehydrogenase (hsd17b), and 3β-hydroxysteroid dehydrogenase (hsd3b). We sampled adult scallops throughout their reproductive phase to compare their degree of maturation with their intensity of mRNA expression. Semi-quantitative RT-PCR analysis revealed a ubiquitous expression of transcripts for steroid metabolizing enzymes (i.e., star, cyp17a, hsd17b, and hsd3b) in peripheral and gonadal tissues. Real-time PCR analysis revealed a high level of expression of star3 and cyp17a genes in gonadal tissues at the early stage of cell differentiation in scallops. Interestingly, mRNA expression of hsd3b and hsd17b genes showed a synchronous pattern related to degree of gonad maturity. These results indicate that both hsd3b and hsd17b genes are likely involved in steroidogenesis in scallops. We therefore believe that these steroid-metabolizing enzymes allow scallops to endogenously produce sex steroids to regulate reproductive events.
Collapse
Affiliation(s)
- Tongchai Thitiphuree
- Laboratory of Aquacultural Biology, Graduate School of Agricultural Science, Tohoku University, 468-1Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Kazue Nagasawa
- Laboratory of Aquacultural Biology, Graduate School of Agricultural Science, Tohoku University, 468-1Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Makoto Osada
- Laboratory of Aquacultural Biology, Graduate School of Agricultural Science, Tohoku University, 468-1Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8572, Japan.
| |
Collapse
|
35
|
Mao J, Zhang X, Zhang W, Tian Y, Wang X, Hao Z, Chang Y. Genome-wide identification, characterization and expression analysis of the MITF gene in Yesso scallops (Patinopecten yessoensis) with different shell colors. Gene 2018; 688:155-162. [PMID: 30552980 DOI: 10.1016/j.gene.2018.11.096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/25/2018] [Accepted: 11/28/2018] [Indexed: 01/03/2023]
Abstract
The microphthalmia-associated transcription factor (MITF) is the center of the regulator network of melanin synthesis in vertebrates. However, the role of MITF in shell color formation is poorly studied in mollusks. In the present study, an MITF gene, PyMITF, was first identified at the whole-genome level in Yesso scallop (Patinopecten yessoensis), an evolutionarily and economically important species, the shell color of which shows polymorphism. The PyMITF is a large gene spanning ~37 kb in the genome with 7 introns and 8 exons. A basic helix-loop-helix leucine zipper (bHLH-LZ) domain was detected in the PyMITF protein sequence, which can bind the canonical E-box sequence in the promoter region of the downstream genes. Phylogenetic analysis of the MITFs among vertebrates and invertebrates revealed that the molecular evolution of MITFs was consistent with the species taxonomy. Different expression levels of PyMITF were detected among different shell color strains, indicating the important role of PyMITF involved in shell pigmentation. Besides, PyMITF was expressed at a significantly higher level in the central mantle than that in the edge mantle, proving the participation of the central mantle in shell color formation in molecular level for the first time. The work provides valuable information for the molecular mechanism study of shell color formation.
Collapse
Affiliation(s)
- Junxia Mao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xiaosen Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Wenjing Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Xubo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Zhenlin Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
| |
Collapse
|
36
|
Paul S, Heckmann LH, Sørensen JG, Holmstrup M, Arumugaperumal A, Sivasubramaniam S. Transcriptome sequencing, de novo assembly and annotation of the freeze tolerant earthworm, Dendrobaena octaedra. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
37
|
Shi Y, Xu M, Huang J, Zhang H, Liu W, Ou Z, He M. Transcriptome analysis of mantle tissues reveals potential biomineralization-related genes in Tectus pyramis Born. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:131-144. [PMID: 30469052 DOI: 10.1016/j.cbd.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/11/2018] [Indexed: 10/27/2022]
Abstract
The marine mollusk Tectus pyramis is a valuable shellfish primarily distributed in the tropical waters of the South China Sea, as well as in the Indo-Pacific Ocean and areas near the southern portion of the Japanese Peninsula. Despite major economic interest in this mollusk, limited genomic resources are available for this species, which has prevented studies of the molecular mechanism, such as biomineralization. Here, we report the first comprehensive transcript dataset of T. pyramis mantle tissue. From a total of 16,801,141 reads, 173,671 unique transcripts were assembled, which provides new genomic resources for the understanding of biomineralization in T. pyramis. The most abundant unique sequences of the top 30 most highly expressed genes were annotated as shematrin, while other highly expressed genes included glycine-rich protein and shematrin-1. Based on transcriptome annotation and Gene Ontology classification, 130 biomineralization-related genes were found including members of the BMP (bone morphogenetic proteins), calmodulin, perlucin, and shematrin families, as well as mantle genes, nacrein, and MSI60. The results of qPCR showed that 14 of 24 examined genes were highly expressed in the mantle. A phylogenetic tree of BMP, perlucin, shematrin proteins revealed conservation of their structure and functions and indicated that some members participated in biomineralization in T. pyramis. Taken together, the results presented herein will be useful in studies of molecular mechanisms and pathways of biomineralization in T. pyramis, as well as provide new insight into the mechanisms of biomineralization in gastropods.
Collapse
Affiliation(s)
- Yu Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Meng Xu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jing Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenguang Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Zekui Ou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
| |
Collapse
|
38
|
Vikashini B, Shanthi A, Ghosh Dasgupta M. Identification and expression profiling of genes governing lignin biosynthesis in Casuarina equisetifolia L. Gene 2018; 676:37-46. [PMID: 30201104 DOI: 10.1016/j.gene.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 11/24/2022]
Abstract
Casuarina equisetifolia L. is an important multi-purpose, fast growing and widely planted tree species native to tropical and subtropical coastlines of Australia, Southeast Asia, Malaysia, Melanesia, Polynesia and New Caledonia. It is a nitrogen-fixing tree mainly used for charcoal making, construction poles, landscaping, timber, pulp, firewood, windbreaks, shelterbelts, soil erosion and sand dune stabilization. Casuarina wood is presently used for paper and pulp production. Raw material with reduced lignin is highly preferred to increase the pulp yield. Hence, understanding the molecular regulation of wood formation in this tree species is vital for selecting industrially suitable phenotypes for breeding programs. The lignin biosynthetic pathway has been extensively studied in tree species like Eucalypts, poplars, pines, Picea, Betula and Acacia sp. However, studies on wood formation at molecular level is presently lacking in casuarinas. Hence, in the present study, the transcriptome of the developing secondary tissues of 15 years old Casuarina equiseitfolia subsp. equisetifolia was sequenced, de novo assembled, annotated and mapped to functional pathways. Transcriptome sequencing generated a total of 26,985 transcripts mapped to 31 pathways. Mining of the annotated data identified nine genes involved in lignin biosynthesis pathway and relative expression of the transcripts in four tissues including scale-like leaves, needle-like brachlets, wood and root were documented. The expression of CeCCR1 and CeF5H were found to be significantly high in wood tissues, while maximum expression of CeHCT was documented in stem. Additionally, CeTUBA and CeH2A were identified as the most stable reference transcript for normalization of qRT-PCR data in C. equisetifolia. The present study is the first wood genomic resource in C. equisetifolia, which will be valuable for functional genomics research in this genus.
Collapse
Affiliation(s)
| | - Arunachalam Shanthi
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, Tamil Nadu, India
| | - Modhumita Ghosh Dasgupta
- Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore 641002, Tamil Nadu, India.
| |
Collapse
|
39
|
Lv J, Jiao W, Guo H, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S. HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Res 2018; 28:1919-1930. [PMID: 30409770 PMCID: PMC6280760 DOI: 10.1101/gr.235820.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.
Collapse
Affiliation(s)
- Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haobing Guo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
40
|
Xu DP, Jiang SL, Zhao CS, Fang DA, Hu HY. Comparative transcriptomics analysis of the river pufferfish (Takifugu obscurus) by tributyltin exposure: Clues for revealing its toxic injury mechanism. FISH & SHELLFISH IMMUNOLOGY 2018; 82:536-543. [PMID: 30170111 DOI: 10.1016/j.fsi.2018.08.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
TBT residual in water had become a noticeable ecological problem for aquatic ecosystems. The river pufferfish (Takifugu obscurus) is a kind of an anadromous fish species and widely distributed in the East China Sea and the Yellow Sea. Because of the water contamination, the pufferfish wild resource had a sudden decline in recent years. Therefore, the study on the response of pufferfish to the TBT exposure may contribute to reveal toxic injury mechanism of T. obscurus under TBT exposure. In this study, the transcriptional library of T. obscurus liver and gill was constructed and sequenced by an improved Illumina HiseqX10 high-throughput sequencing platform under different concentrations of TBT acute stress. The blood cell numbers distinctly decreased after TBT exposure, showing the adverse effects of TBT invasion and self-adjusting ability of the pufferfish. The production of reactive oxygen species increased, demonstrating the oxidation resistance of T. obscurus when exposed to TBT. The obtained data were compared with the genome data of Takifugu rubripes and transcriptional resource database. On this basis, gene function annotation, analysis and classification were carried out by bioinformatics method, and differential genes related to toxic injury function were screened out. Meanwhile, new toxic related genes and related signal pathways were sought to provide new theoretical guidance for the pathogenesis of T. obscurus exposed to TBT. This study not only enriched the transcriptome data of T. obscurus under environmental stress, but also provided a new research method for the response mechanism of T. obscurus under the stimulation of environmental factors.
Collapse
Affiliation(s)
- Dong-Po Xu
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
| | - Shu-Lun Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Xuejiali 69, Wuxi, 214128, China
| | - Chang-Sheng Zhao
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
| | - Di-An Fang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu, 214081, China
| | - Hao-Yuan Hu
- Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China.
| |
Collapse
|
41
|
Ma C, Ma H, Xu G, Feng C, Ma L, Wang L. De novo sequencing of the Antarctic krill (Euphausia superba) transcriptome to identify functional genes and molecular markers. J Genet 2018. [DOI: 10.1007/s12041-018-0967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
42
|
Guo H, Li Y, Zhang M, Li R, Li W, Lou J, Bao Z, Wang Y. Expression of Cathepsin F in response to bacterial challenges in Yesso scallop Patinopecten yessoensis. FISH & SHELLFISH IMMUNOLOGY 2018; 80:141-147. [PMID: 29879509 DOI: 10.1016/j.fsi.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 06/08/2023]
Abstract
Cathepsin F is a unique papain cysteine proteinase with highly conserved structures: catalytic triad and a cystatin domain contained in the elongated N-terminal pro-region. It has been reported that cathepsin F is associated with the establishment of innate immune in several vertebrate including fish in aquaculture, but not known in bivalves. In this study, we firstly identified and characterized cathepsin F in the Yesso scallop (Patinopecten yessoensis). The protein structural and phylogenetic analyses were then conducted to determine its identity and evolutionary position. We've also investigated the expression levels of cathepsin F gene at different embryonic developmental stages, in healthy adult tissues and especially in the hemocytes and hepatopancreas after Gram-positive (Micrococcus luteus) and negative (Vibrio anguillarum) challenges using quantitative real-time PCR (qPCR). Cathepsin F was significantly up-regulated 3 h after infection of V. anguillarum in hemocytes, suggesting its participation in immune response. Our findings have provided strong evidence that cathepsin F may be a good target for enhancing the immune activity in Yesso scallop.
Collapse
Affiliation(s)
- Haobing Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yangping Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Meiwei Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Ruojiao Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Wanru Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiarun Lou
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| |
Collapse
|
43
|
Wang S, Li X, Li T, Wang H, Zhang X, Lou J, Xing Q, Hu X, Bao Z. The GRP94 gene of Yesso scallop (Patinopecten yessoensis): Characterization and expression regulation in response to thermal and bacterial stresses. FISH & SHELLFISH IMMUNOLOGY 2018; 80:443-451. [PMID: 29894740 DOI: 10.1016/j.fsi.2018.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/09/2018] [Indexed: 06/08/2023]
Abstract
The 94-kDa glucose-regulated protein (GRP94) belonging to the HSP90 family is an endoplasmic reticulum (ER) chaperone. It plays critical roles in ER quality control, and has been implicated as a specialized immune chaperone to regulate both innate and adaptive immunity. In this study, we identified and characterized a GRP94 gene (PyGRP94) from Yesso scallop (Patinopecten yessoensis). The protein sequence of PyGRP94 is highly conserved with its homologs in vertebrates, with a signal sequence in N-terminal, an ER retrieval signal sequence in C-terminal and a HATPase_c domain. Expression analysis suggests that PyGRP94 transcripts in early embryos are maternally derived and the zygotic expression is started from D-shaped larvae. This gene is also expressed in almost all the adult tissues examined except smooth muscle, with the highest expression level in hemocytes. Besides, PyGRP94 was demonstrated to be induced by heat shock and both Gram-positive (Micrococcus luteus) and Gram-negative (Vibrio anguillarum) bacterial infection, with much more dramatic changes being observed after V. anguillarum challenge. Our results suggest the involvement of PyGRP94 in response to thermal stress, and that it might play an important role in the innate immune defense of scallop.
Collapse
Affiliation(s)
- Shuyue Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xu Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Tingting Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Huizhen Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiangchao Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Qiang Xing
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
44
|
Ma C, Ma H, Xu G, Feng C, Ma L, Wang L. De novo sequencing of the Antarctic krill ( Euphausia superba) transcriptome to identify functional genes and molecular markers. J Genet 2018; 97:995-999. [PMID: 30262712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
To provide massive genetic resources for the Antarctic krill (Euphausia superba), we sequenced and analysed the transcriptome by using high-throughput Illumina paired-end sequencing technology. A total of 77.1 million clean reads representing ~11.0Gb data were generated. The average length of these reads was 142 bp. De novo assembly yielded 125,211 transcripts with a N50 of 690 bp. Further analysis produced 106,250 unigenes, of which 31,683 were annotated based on protein homology searches against protein databases. Gene ontology analysis showed that ion binding, organic substance, metabolic process, and cell part were the most abundantly used terms in molecular function, biological process and cellular component categories, respectively. In addition, 3067 unigenes were mapped onto 311 signal pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, 15,224 simple sequence repeats were identified from 13,535 transcripts, and 103,593 single-nucleotide polymorphisms were found from 21.6% of total transcripts. These genetic resources obtained in this study forms a good foundation for investigating gene function, and evaluating population genetic diversity for this important Southern Ocean fisheries resource, E. superba.
Collapse
Affiliation(s)
- Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, People's Republic of China. ;
| | | | | | | | | | | |
Collapse
|
45
|
The ultrastructural features of embryonic and early larval development in Yesso scallop, Mizuhopecten yessoensis. Tissue Cell 2018; 53:76-86. [DOI: 10.1016/j.tice.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/01/2018] [Accepted: 06/11/2018] [Indexed: 11/23/2022]
|
46
|
Liao H, Wang J, Xun X, Zhao L, Yang Z, Zhu X, Xing Q, Huang X, Bao Z. Identification and characterization of TEP family genes in Yesso scallop (Patinopecten yessoensis) and their diverse expression patterns in response to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2018; 79:327-339. [PMID: 29803664 DOI: 10.1016/j.fsi.2018.05.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Thioester-containing protein (TEP) family members are characterized by their unique intrachain β-cysteinyl-γ-glutamyl thioesters, and they play important roles in innate immune responses. Although significant effects of TEP members on immunity have been reported in most vertebrates, as well as certain invertebrates, the complete TEP family has not been systematically characterized in scallops. In this study, five TEP family genes (PyC3, PyA2M, PyTEP1, PyTEP2 and PyCD109) were identified from Yesso scallop (Patinopecten yessoensis) through whole-genome scanning, including one pair of tandem duplications located on the same scaffold. Phylogenetic and protein structural analyses were performed to determine the identities and evolutionary relationships of the five genes (PyTEPs). The vast distribution of PyTEPs in TEP subfamilies confirmed that the Yesso scallop contains relatively comprehensive types of TEP members in evolution. The expression profiles of PyTEPs were determined in hemocytes after bacterial infection with gram-positive (Micrococcus luteus) and gram-negative (Vibrio anguillarum) using quantitative real-time PCR (qRT-PCR). Expression analysis revealed that the PyTEP genes exhibited disparate expression patterns in response to the infection by gram bacteria. A majority of PyTEP genes were overexpressed after bacterial stimulation at most time points, especially the notable elevation displayed by duplicated genes after V. anguillarum challenge. Interestingly, at different infection times, PyTEP1 and PyTEP2 shared analogous expression patterns, as did PyC3 and PyCD109. Taken together, these results help to characterize gene duplication and the evolutionary origin of PyTEPs and supplied valuable resources for elucidating their versatile roles in bivalve innate immune responses to bacterial pathogen challenges.
Collapse
Affiliation(s)
- Huan Liao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jing Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xiaogang Xun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Liang Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xinghai Zhu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Qiang Xing
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiaoting Huang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| |
Collapse
|
47
|
Ning X, Feng L, Li X, Wang S, Zhang M, Wang S, Zhang L, Hu X, Bao Z. The scallop IGF2 mRNA-binding protein gene PyIMP and association of a synonymous mutation with growth traits. Genes Genet Syst 2018; 93:91-100. [PMID: 29998907 DOI: 10.1266/ggs.17-00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Insulin-like growth factor 2 mRNA-binding proteins (IMPs) function in localization, stability and translational control of their target RNAs. In this study, we identified an IMP gene (PyIMP) from Yesso scallop, Patinopecten yessoensis. The complete DNA sequence of PyIMP was 22,875 bp, consisting of seventeen exons and sixteen introns. The full-length cDNA sequence was 3,293 bp, with an open reading frame of 1,776 bp, encoding 592 amino acids. PyIMP exhibited characters typical of IMPs, namely two RNA recognition motifs and four hnRNP K homology domains. Real-time quantitative reverse transcription PCR analysis indicated that PyIMP was universally expressed, with higher expression levels in the gonad of adult scallops, and in gastrulae and trochophore larvae at developmental stages. A synonymous mutation SNP, c.852A>G, which showed significant associations with growth traits of Yesso scallop, was identified in this gene. Scallops with the AA genotype at this locus had significantly higher trait values than those with the GG genotype for shell length, shell height, body weight, soft tissue weight and striated muscle weight (P < 0.05). Meanwhile, the expression of PyIMP in AA type scallops was significantly higher than that in the GG type, implying a positive effect of PyIMP on scallop growth. PyIMP represents the first mRNA-binding protein gene characterized in mollusks, and SNP c.852A>G will be useful for a better understanding of the role of mRNA-binding proteins in bivalves and for scallop breeding.
Collapse
Affiliation(s)
- Xianhui Ning
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Liying Feng
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Xue Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Shuyue Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Mengran Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China
| | - Shi Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology
| | - Lingling Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
| | - Xiaoli Hu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology
| |
Collapse
|
48
|
Milan M, Dalla Rovere G, Smits M, Ferraresso S, Pastore P, Marin MG, Bogialli S, Patarnello T, Bargelloni L, Matozzo V. Ecotoxicological effects of the herbicide glyphosate in non-target aquatic species: Transcriptional responses in the mussel Mytilus galloprovincialis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 237:442-451. [PMID: 29505984 DOI: 10.1016/j.envpol.2018.02.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/26/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Glyphosate has been the most widely used herbicide worldwide over the last three decades, raising increasing concerns for its potential impacts on environmental and human health. Recent studies revealed that glyphosate occurs in soil, surface water, and groundwater, and residues are found at all levels of the food chain, such as drinking water, plants, animals, and even in humans. While research has demonstrated that glyphosate can induce a broad range of biological effects in exposed organisms, the global molecular mechanisms of action still need to be elucidated, in particular for marine species. In this study, we characterized for the first time the molecular mechanisms of action of glyphosate in a marine bivalve species after exposure to environmentally realistic concentrations. To reach such a goal, Mediterranean mussels Mytilus galloprovincialis, an ecologically and economically relevant species, were exposed for 21 days to 10, 100, and 1000 μg/L and digestive gland transcriptional profiles were investigated through RNA-seq. Differential expression analysis identified a total of 111, 124, and 211 differentially regulated transcripts at glyphosate concentrations of 10, 100, and 1000 μg/L, respectively. Five genes were found consistently differentially expressed at all investigated concentrations, including SERP2, which plays a role in the protection of unfolded target proteins against degradation, the antiapoptotic protein GIMAP5, and MTMR14, which is involved in macroautophagy. Functional analysis of differentially expressed genes reveals the disruption of several key biological processes, such as energy metabolism and Ca2+ homeostasis, cell signalling, and endoplasmic reticulum stress response. Together, the results obtained suggest that the presence of glyphosate in the marine ecosystem should raise particular concern because of its significant effects even at the lowest concentration.
Collapse
Affiliation(s)
- M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy.
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - M Smits
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy; Marine Environmental Science Laboratory (LEMAR), Université de Bretagne Occidentale -Rue Dumont d'Urville, 29280 Plouzané - IUEM Technopole Brest-Iroise, France
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - P Pastore
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - S Bogialli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| |
Collapse
|
49
|
Cao S, Zhu L, Nie H, Yin M, Liu G, Yan X. De novo assembly, gene annotation, and marker development using Illumina paired-end transcriptome sequencing in the Crassadoma gigantea. Gene 2018. [PMID: 29524581 DOI: 10.1016/j.gene.2018.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Crassadoma gigantea is an important commercial marine bivalve species in Baja California and Mexico. In this study, we have applied RNA-Seq technology to profile the transcriptome of the C. gigantea for the first time. A total of 80,832,518 raw reads were produced from a Illumina HiSeq4000 platform, and 77,306,198 (95.64%) clean reads were generated after trimming the adaptor sequences. The transcriptome assembled into 158,855 transcripts with an N50 size of 1995 bp and an average size of 1008 bp. A number of DNA repair related genes, such as MSH3, EGF, TGF, IGF, FGF, encoding different groups of growth factors were found in the transcriptome data of C. gigantean. In addition, immune related genes Toll-like receptor (TLR) including TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, and TLR9 was also observed in C. gigantean. A set of 12 polymorphic microsatellite loci were firstly developed and characterized in C. gigantea. The results show that the number of alleles and expected heterozygosity ranged from 3 to 9 and from 0.254 to 0.820, respectively. The average polymorphic information content was 0.790. These microsatellite loci will facilitate future studies of population structure and conservation genetics in this species.
Collapse
Affiliation(s)
- Shanmao Cao
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Lijie Zhu
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
| | - Minghao Yin
- Dalian City Oceanic and Fishery Administration, 100000 Dalian, China
| | - Gang Liu
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| |
Collapse
|
50
|
Galindo-Torres P, García-Gasca A, Llera-Herrera R, Escobedo-Fregoso C, Abreu-Goodger C, Ibarra AM. Sex determination and differentiation genes in a functional hermaphrodite scallop, Nodipecten subnodosus. Mar Genomics 2017; 37:161-175. [PMID: 29239804 DOI: 10.1016/j.margen.2017.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/23/2017] [Accepted: 11/16/2017] [Indexed: 01/12/2023]
Abstract
The lion-paw, Nodipecten subnodosus is one of three scallop species commercially exploited on the west coast of the Peninsula of Baja California. Because nothing is known about sex determination and sexual differentiation in hermaphrodite scallops, in the present work, a global transcriptomic analysis was performed in two early developmental stages, settling eyed-larvae and spat, as well as in three tissues (undifferentiated gonad, digestive gland, and adductor muscle). Over 27 million Illumina paired-end reads were obtained through the MiSeq platform. After processing the reads a total of 243,774 transcripts were assembled with an N50 of 980 and an average length of 775nt. A total of 43,252 proteins were inferred and 36,103 transcripts had at least one homolog in the SwissProt database according to a blastx search. After differential expression analyses and GO annotations it was possible to identify several sex-related genes in the scallop, including one known to be involved in the sex determination pathway of the hermaphrodite model organism Caenorhabditis elegans, N. subnodosus-sex1 (Ns-sex1). Other interesting sex determination and differentiation genes were Ns-dmrta2, Ns-sox9, Ns-wnt4, Ns-doa, Ns-ovo, Ns-vir, among others. Most of these genes were mainly expressed in the testis region, suggesting their participation in male gonad region sex differentiation. These results represent the first available information on the genetics of sex determination and differentiation in a functional hermaphrodite scallop.
Collapse
Affiliation(s)
- Pavel Galindo-Torres
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No.195, La Paz, Baja California Sur 23096, Mexico.
| | - Alejandra García-Gasca
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos s/n, Estero del Yugo, Mazatlán, Sinaloa 82000, Mexico.
| | - Raúl Llera-Herrera
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos s/n, Estero del Yugo, Mazatlán, Sinaloa 82000, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACYT), Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico.
| | - Cristina Escobedo-Fregoso
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No.195, La Paz, Baja California Sur 23096, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACYT), Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico.
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Km 9.6 Libramiento Norte, Irapuato, Guanajuato 36824, Mexico.
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No.195, La Paz, Baja California Sur 23096, Mexico.
| |
Collapse
|