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Cai Z, Liu S, Wang W, Wang R, Miao X, Song P, Shan B, Wang L, Li Y, Lin L. Comparative transcriptome sequencing analysis of female and male Decapterus macrosoma. PeerJ 2022; 10:e14342. [PMID: 36389430 PMCID: PMC9651050 DOI: 10.7717/peerj.14342] [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: 06/20/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022] Open
Abstract
Sexual growth dimorphism is a common phenomenon in teleost fish and has led to many reproductive strategies. Growth- and sex-related gene research in teleost fish would broaden our understanding of the process. In this study, transcriptome sequencing of shortfin scad Decapterus macrosoma was performed for the first time, and a high-quality reference transcriptome was constructed. After identification and assembly, a total of 58,475 nonredundant unigenes were obtained with an N50 length of 2,266 bp, and 28,174 unigenes were successfully annotated with multiple public databases. BUSCO analysis determined a level of 92.9% completeness for the assembled transcriptome. Gene expression analysis revealed 2,345 differentially expressed genes (DEGs) in the female and male D. macrosoma, 1,150 of which were female-biased DEGs, and 1,195 unigenes were male-biased DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were mainly involved in biological processes including protein synthesis, growth, rhythmic processes, immune defense, and vitellogenesis. Then, we identified many growth- and sex-related genes, including Igf, Fabps, EF-hand family genes, Zp3, Zp4 and Vg. In addition, a total of 19,573 simple sequence repeats (SSRs) were screened and identified from the transcriptome sequences. The results of this study can provide valuable information on growth- and sex-related genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.
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Affiliation(s)
- Zizi Cai
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Shigang Liu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Rui Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xing Miao
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Puqing Song
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Binbin Shan
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Liangming Wang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China
| | - Longshan Lin
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China,Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen, China
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Zhang Y, Nie H, Yin Z, Yan X. Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum). BMC Genomics 2022; 23:676. [PMID: 36175832 PMCID: PMC9524096 DOI: 10.1186/s12864-022-08813-0] [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: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background The Manila clam Ruditapesphilippinarum is one of the most economically important marine shellfish. However, the molecular mechanisms of early development in Manila clams are largely unknown. In this study, we collected samples from 13 stages of early development in Manila clam and compared the mRNA expression pattern between samples by RNA-seq techniques. Results We applied RNA-seq technology to 13 embryonic and larval stages of the Manila clam to identify critical genes and pathways involved in their development and biological characteristics. Important genes associated with different morphologies during the early fertilized egg, cell division, cell differentiation, hatching, and metamorphosis stages were identified. We detected the highest number of differentially expressed genes in the comparison of the pediveliger and single pipe juvenile stages, which is a time when biological characteristics greatly change during metamorphosis. Gene Ontology (GO) enrichment analysis showed that expression levels of microtubule protein-related molecules and Rho genes were upregulated and that GO terms such as ribosome, translation, and organelle were enriched in the early development stages of the Manila clam. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the foxo, wnt, and transforming growth factor-beta pathways were significantly enriched during early development. These results provide insights into the molecular mechanisms at work during different periods of early development of Manila clams. Conclusion These transcriptomic data provide clues to the molecular mechanisms underlying the development of Manila clam larvae. These results will help to improve Manila clam reproduction and development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08813-0.
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Affiliation(s)
- Yanming Zhang
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China.,Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China. .,Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China.
| | - Zhihui Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China.,Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China.,Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, 116023, Dalian, China
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Wan H, Zhong J, Zhang Z, Xie Y, Wang Y. Characterization of the foxl2 gene involved in the vtg expression in mud crab (Scylla paramamosain). Gene 2021; 798:145807. [PMID: 34224832 DOI: 10.1016/j.gene.2021.145807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 01/01/2023]
Abstract
Forkhead box protein L2 (Foxl2) is involved in multiple physiological processes, such as ovarian development, granulosa cell differentiation, ovarian follicle development, and oocyte growth. In this study, a Spfoxl2 gene encoded 530 amino acid protein with characteristic forkhead (FH) domain was identified from transcriptome data of mud crab Scylla paramamosain and validated the accuracy by PCR technology. Meanwhile, the orthologues of the Spfoxl2 gene in other 14 crustacean species were identified with the same method. Further multiple sequence alignment analysis revealed the Foxl2 was highly conserved, especially in the FH domain, even completely identical in several species. Besides, the semi-quantitative PCR (Sq-PCR) result showed Spfoxl2 gene was mainly expressed in the gonad (testis and ovary). Further quantitative real-time PCR (qRT-PCR) result demonstrated its expression level in the testis was significantly higher than that in the ovary (p < 0.01). In addition, the qRT-PCR result showed that in zoea V, megalopa, and larval I, the expression level of Spfoxl2 in megalopa is the highest. In addition, a putative Foxl2 binding site was identified on the promoter region of Spvtg, and knockdown of Spfoxl2 mediated by RNAi technology increased the expression of Spvtg in the ovary, suggesting Spfoxl2 might be the upstream negative regulator of Spvtg. Overall, this study provided new insights into the role of Spfoxl2 in ovary development through regulating Spvtg expression in S. paramamosain.
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Affiliation(s)
- Haifu Wan
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Jinying Zhong
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yichao Xie
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen 361021, China.
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Comprehensive phylogeny of Konosirus punctatus (Clupeiformes: Clupeidae) based on transcriptomic data. Biosci Rep 2021; 41:228456. [PMID: 33899917 PMCID: PMC8128103 DOI: 10.1042/bsr20210455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/03/2022] Open
Abstract
Konosirus punctatus is an important species for the structure of marine ecosystems. Meanwhile, it is a native species in the northwest Pacific Ocean and supports important commercial fishery. In the present study, we generated the whole transcriptome of K. punctatus from combined tissues (muscle, liver, gill, heart, kidney, swim bladder and sexual gland) using Illumina RNA-seq technology and a total of 46087110 clean reads were obtained, corresponding to 6531521430 nucleotides. Meanwhile, 10000 clean reads were randomly selected and compared with NT database to examine the possible contamination. Results showed that 6754 clean reads were distributed among some species closely related with K. punctatus, indicating no-pollution. De novo assembly was performed and all clean reads were assembled to produce 71610 longest unigenes with an N50 of 906 bp. Among all the unigenes, 43974 unigenes were annotated in at least one database and 3172 unigenes were annotated in all databases. All unigenes were further analyzed to predict the gene structure and we have obtained a total of 54864 coding sequences (CDSs) and 17326 simple sequence repeats (SSRs). Saturation analyses were applied to evaluate the accuracy of gene expression and we hypothesized that the detection of gene expression might be effective. Finally, single-copy orthologous genes were applied to construct the phylogenetic relationship of K. punctatus. Results showed that K. punctatus diverged from the common ancestor with Alosa alosa, Alosa pseudoharengus and Sardina pilchardus at approx. 61.16–92.52 MYA. The present study will provide a foundational molecular information for the biological research of K. punctatus.
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Shan B, Liu Y, Yang C, Zhao Y, Sun D. Comparative transcriptomic analysis for identification of candidate sex-related genes and pathways in Crimson seabream (Parargyrops edita). Sci Rep 2021; 11:1077. [PMID: 33441831 PMCID: PMC7806868 DOI: 10.1038/s41598-020-80282-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Teleost fishes display the largest array of sex-determining systems among animals, resulting in various reproductive strategies. Research on sex-related genes in teleosts will broaden our understanding of the process, and provide important insight into the plasticity of the sex determination process in vertebrates in general. Crimson seabream (Parargyrops edita Tanaka, 1916) is one of the most valuable and abundant fish resources throughout Asia. However, little genomic information on P. edita is available. In the present study, the transcriptomes of male and female P. edita were sequenced with RNA-seq technology. A total of 388,683,472 reads were generated from the libraries. After filtering and assembling, a total of 79,775 non redundant unigenes were obtained with an N50 of 2,921 bp. The unigenes were annotated with multiple public databases, including NT (53,556, 67.13%), NR (54,092, 67.81%), Swiss-Prot (45,265, 56.74%), KOG (41,274, 51.74%), KEGG (46,302, 58.04%), and GO (11,056, 13.86%) databases. Comparison of the unigenes of different sexes of P. edita revealed that 11,676 unigenes (9,335 in females, 2,341 in males) were differentially expressed between males and females. Of these, 5,463 were specifically expressed in females, and 1,134 were specifically expressed in males. In addition, the expression levels of ten unigenes were confirmed to validate the transcriptomic data by qRT-PCR. Moreover, 34,473 simple sequence repeats (SSRs) were identified in SSR-containing sequences, and 50 loci were randomly selected for primer development. Of these, 36 loci were successfully amplified, and 19 loci were polymorphic. Finally, our comparative analysis identified many sex-related genes (zps, amh, gsdf, sox4, cyp19a, etc.) and pathways (MAPK signaling pathway, p53 signaling pathway, etc.) of P. edita. This informative transcriptomic analysis provides valuable data to increase genomic resources of P. edita. The results will be useful for clarifying the molecular mechanism of sex determination and for future functional analyses of sex-associated genes.
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Affiliation(s)
- Binbin Shan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Yan Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Changping Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Yu Zhao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
| | - Dianrong Sun
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture Rural Affairs, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, China.
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.
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Wan H, Liao J, Zhang Z, Zeng X, Liang K, Wang Y. Molecular cloning, characterization, and expression analysis of a sex-biased transcriptional factor sox9 gene of mud crab Scylla paramamosain. Gene 2021; 774:145423. [PMID: 33434625 DOI: 10.1016/j.gene.2021.145423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 01/10/2023]
Abstract
Sox9 gene, a crucial member of the Sox gene family, is present in various organisms and involved in many physiological processes, especially in sex determination and gonad development. In this study, we reported a sox9 gene (designated as Spsox9) from Scylla paramamosain through analyzing published gonad transcriptome data. Meanwhile, the accuracy was validated by PCR technology, and the 3' sequences were cloned with 3' RACE technology. The full-length cDNA of Spsox9 is 2843 bp, consisting of a 243 bp 5' UTR, an 1124 bp 3' UTR, and a 1476 bp ORF encoding 491 amino acids. Furthermore, to better understand its conservation among crustacean species, the sox9 gene ortholog was identified in several other crustaceans species with their published transcriptome data, respectively. All of the Sox9 proteins identified in the current study had the common feature of Sox proteins (HMG domain) and were highly conserved among analyzed crustacean species. In all examined tissues, the Spsox9 was mainly expressed in the gonad (testis and ovary), eyestalk, and cerebral ganglion. During embryo development, Spsox9 was highly expressed in 5 pairs of appendages, 7 pairs of appendages, and eye-pigment formation stage. During ovary development, the expression level of Spsox9 remained stable in the first 4 stages (O1-O4) and decreased in the tertiary vitellogenesis (O5) stage. During testis development, the expression level of Spsox9 was highest in the spermatid stage (T2) and was significantly different from that in the spermatocyte stage (T1) and mature sperm stage (T3) (p < 0.05). In addition, Spsox9 exhibited a sex-biased expression pattern in T1 and O1. These present results indicated that the Spsox9 gene might play crucial roles in the gonad and embryo development of mud crab.
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Affiliation(s)
- Haifu Wan
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen 361021, China
| | - Jiaqian Liao
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen 361021, China
| | - Ziping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xianyuan Zeng
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen 361021, China
| | - Keying Liang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen 361021, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Jimei University, Xiamen 361021, China.
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7
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Sun Z, Lou F, Zhang Y, Song N. Gill Transcriptome Sequencing and De Novo Annotation of Acanthogobius ommaturus in Response to Salinity Stress. Genes (Basel) 2020; 11:genes11060631. [PMID: 32521805 PMCID: PMC7349121 DOI: 10.3390/genes11060631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/23/2020] [Accepted: 06/04/2020] [Indexed: 01/17/2023] Open
Abstract
Acanthogobius ommaturus is a euryhaline fish widely distributed in coastal, bay and estuarine areas, showing a strong tolerance to salinity. In order to understand the mechanism of adaptation to salinity stress, RNA-seq was used to compare the transcriptome responses of Acanthogobius ommaturus to the changes of salinity. Four salinity gradients, 0 psu, 15 psu (control), 30 psu and 45 psu were set to conduct the experiment. In total, 131,225 unigenes were obtained from the gill tissue of A. ommaturus using the Illumina HiSeq 2000 platform (San Diego, USA). Compared with the gene expression profile of the control group, 572 differentially expressed genes (DEGs) were screened, with 150 at 0 psu, 170 at 30 psu, and 252 at 45 psu. Additionally, among these DEGs, Gene Ontology (GO) analysis indicated that binding, metabolic processes and cellular processes were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis detected 3, 5 and 8 pathways related to signal transduction, metabolism, digestive and endocrine systems at 0 psu, 30 psu and 45 psu, respectively. Based on GO enrichment analysis and manual literature searches, the results of the present study indicated that A. ommaturus mainly responded to energy metabolism, ion transport and signal transduction to resist the damage caused by salinity stress. Eight DEGs were randomly selected for further validation by quantitative real-time PCR (qRT-PCR) and the results were consistent with the RNA-seq data.
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Affiliation(s)
| | | | | | - Na Song
- Correspondence: or ; Tel.: +86-532-820-31658
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Artal MC, Pereira KD, Luchessi AD, Okura VK, Henry TB, Marques-Souza H, de Aragão Umbuzeiro G. Transcriptome analysis in Parhyale hawaiensis reveal sex-specific responses to AgNP and AgCl exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113963. [PMID: 32004961 DOI: 10.1016/j.envpol.2020.113963] [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: 08/27/2019] [Revised: 12/09/2019] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Analysis of the transcriptome of organisms exposed to toxicants offers new insights for ecotoxicology, but further research is needed to enhance interpretation of results and effectively incorporate them into useful environmental risk assessments. Factors that must be clarified to improve use of transcriptomics include assessment of the effect of organism sex within the context of toxicant exposure. Amphipods are well recognized as model organisms for toxicity evaluation because of their sensitivity and amenability to laboratory conditions. To investigate whether response to metals in crustaceans differs according to sex we analyzed the amphipod Parhyale hawaiensis after exposure to AgCl and Ag nanoparticles (AgNP) via contaminated food. Gene specific analysis and whole genome transcriptional profile of male and female organisms were performed by both RT-qPCR and RNA-seq. We observed that expression of transcripts of genes glutathione transferase (GST) did not differ among AgCl and AgNP treatments. Significant differences between males and females were observed after exposure to AgCl and AgNP. Males presented twice the number of differentially expressed genes in comparison to females, and more differentially expressed were observed after exposure to AgNP than AgCl treatments in both sexes. The genes that had the greatest change in expression relative to control were those genes related to peptidase and catalytic activity and chitin and carbohydrate metabolic processes. Our study is the first to demonstrate sex specific differences in the transcriptomes of amphipods upon exposure to toxicants and emphasizes the importance of considering gender in ecotoxicology.
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Affiliation(s)
- Mariana Coletty Artal
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil
| | - Karina Danielle Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Augusto Ducati Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, São Paulo, 13484-350, Brazil; Institute of Biosciences, São Paulo State University, Rio Claro, São Paulo, 13506-900, Brazil
| | - Vagner Katsumi Okura
- Life Sciences Core Facility (LaCTAD), University of Campinas, Campinas, São Paulo, 13083-886, Brazil
| | - Theodore Burdick Henry
- Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure, and Society, Heriot-Watt University, EH14 4AS, Edinburgh, Scotland, UK; Center for Environmental Biotechnology, The University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996-1605, United States
| | - Henrique Marques-Souza
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil.
| | - Gisela de Aragão Umbuzeiro
- School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, 05508-000, Brazil; School of Technology, University of Campinas, Limeira, São Paulo, 13484-332, Brazil.
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Lou F, Song N, Han Z, Gao T. Single-molecule real-time (SMRT) sequencing facilitates Tachypleus tridentatus genome annotation. Int J Biol Macromol 2020; 147:89-97. [PMID: 31923512 DOI: 10.1016/j.ijbiomac.2020.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/04/2020] [Accepted: 01/04/2020] [Indexed: 12/19/2022]
Abstract
Tachypleus tridentatus is a keystone species in marine ecosystems. Its hemolymph also provides the limulus amebocyte lysate (LAL) for detection of bacterial endotoxin in human medical service. Here we combined SMRT sequencing and Illumina RNA-seq to characterize the novel isoforms, novel genetic loci, fusion isoforms formation and transcriptome structure and further to unveil the transcriptome complexity of T. tridentatus. We identified 26,705 non-redundancy isoforms form 10,919 genetic loci, including 25,713 novel isoforms, 2403 novel genes and 170 fusion isoforms. In addition, 1578 novel genes and 23,172 novel isoforms were annotated in the NR, Pfam, KOG, COG, eggNOG, Swiss-Prot, KEGG and GO databases. Meanwhile, we have obtained 4671 gene family clustering based on genetic loci. Furthermore, there are 17,296, 4887, 1054, and 1435 APAs, AS events, lncRNAs, and TFs were identified in the T. tridentatus long-read transcriptome and the target genes of 1054 lncRNA sequences were also predicted. Overall, our work firstly provided the long-read transcriptome and these data are very necessary to improve the annotation information of T. tridentatus genome and optimize the boundaries of 12,342 original reference annotated genes. Furthermore, these information are a potential resource to study LAL secretion mechanisms in T. tridentatus.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Ocean University of China, Qingdao, Shandong 266003, China; Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Na Song
- Fishery College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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Jiao T, Yang TT, Wang D, Gao ZQ, Wang JL, Tang BP, Liu QN, Zhang DZ, Dai LS. Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 95:140-150. [PMID: 31629063 DOI: 10.1016/j.fsi.2019.09.072] [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: 08/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.
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Affiliation(s)
- Ting Jiao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China; College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, PR China
| | - Dong Wang
- Instrumental Analysis Center, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Zhen-Qiu Gao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; School of Pharmacy, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Jia-Lian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, PR China.
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224007, PR China.
| | - Li-Shang Dai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, PR China.
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Lou F, Gao T, Han Z. Transcriptome analyses reveal alterations in muscle metabolism, immune responses and reproductive behavior of Japanese mantis shrimp (Oratosquilla oratoria) at different cold temperature. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 32:100615. [PMID: 31419604 DOI: 10.1016/j.cbd.2019.100615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/28/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Low temperature reduction is thought to cause widespread effects on the physical and behavioral traits of marine organisms, which include metabolic processes, immune responses, and reproductive behavior. Crustaceans are generally considered sensitive to temperature reduction due to the lack of efficient regulators. To better understand the molecular regulatory mechanisms of crustacean exposure to cold stress, Japanese mantis shrimp (Oratosquilla oratoria) was chosen as a representative crustacean. Transcriptomic responses in O. oratoria from five temperatures (25 °C, 22 °C, 19 °C, 16 °C, and 13 °C) were studied using RNA-seq. A total of 64.91 Gb of clean transcriptomic data were generated in 10 libraries and then spliced into 52,107 unigenes with an average length of 1089 bp and an N50 length of 1872 bp. A total of 14,841 unigenes was annotated in at least one database using Blastx alignment. Compared with the control temperature (25 °C), 7, 21, 58, and 236 unigenes were significantly differentially expressed at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. GO analysis showed that 6, 20, 27, and 35 terms were significantly enriched at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. In addition, 2, 5, 2, and 10 significant pathways were presented at 22 °C, 19 °C, 16 °C, and 13 °C, respectively. Combining NR, GO, and KEGG annotation information, many genes significantly differentially expressed at low temperatures may be associated with metabolic processes, immune response, and reproductive behavior. Additionally, we reconstructed the phylogenetic relationship based on 366 orthologous genes and the predicted differentiation time of O. oratoria and P. vannamei range from 212.82 to 365.30 Mya. Furthermore, 16 orthologous genes were identified as PSGs and 30 orthologous genes were identified as FEGs and these adaptive genes were associated with energy metabolism, stress response and immunity, and multiple cellular processing. These results provide fundamental information about molecular mechanisms regulating cold stress response of O. oratoria.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China; Fishery College, Ocean University of China, Qingdao, Shandong 266003, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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