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Cui X, Yang M, Li C, An B, Mu S, Zhang H, Chen Y, Li X, Kang X. Assessment of genetic diversity and population structure of Neocaridina denticulata sinensis in the Baiyangdian drainage area, China, using microsatellite markers and mitochondrial cox1 gene sequences. Gene 2023:147534. [PMID: 37286018 DOI: 10.1016/j.gene.2023.147534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
Neocaridina denticulata sinensis is a crustacean of major economic significance in the Baiyangdian drainage area. In this study, the first assessment of N. denticulata sinensis genetic diversity and population structure was performed based on sequence analysis of nine polymorphic microsatellite loci and the mitochondrial cytochrome oxidase subunit I (cox1) gene. Samples (n = 192) were collected from four different regions in the Baiyangdian drainage area i.e., Baiyangdian Lake, Jumahe River, Xidayang Reservoir, and Fuhe River. Microsatellite loci analysis identified high levels of genetic diversity represented by observed heterozygosity (Ho) of 0.6865∼0.9583, expected heterozygosity (He) of 0.7151∼0.8723, and polymorphism information content (PIC) of 0.6676∼0.8585. Based on the analysis of cox1 sequences, haplotype diversity (Hd) ranged from 0.568 to 0.853 while nucleotide diversity (π) ranged from 0.0029 to 0.2236. Furthermore, there was no evidence of expansion events in the N. denticulata sinensis populations. Pairwise FST revealed pronounced genetic differentiation, and clustering analyses showed defined genetic structures within the N. denticulata sinensis population. Three groups were identified from four sampled stocks, with Xidayang reservoir, and Fuhe river populations clustered in the same group. This work identified novel molecular markers and provided an important reference to guide management strategies to assist conservation of N. denticulata sinensis resources.
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Affiliation(s)
- Xiaodong Cui
- College of Life Sciences, Hebei University, Baoding, China
| | - Mei Yang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chunyu Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Bo An
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Han Zhang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yongxia Chen
- College of Life Sciences, Hebei University, Baoding, China
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China.
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Zhang X, Zhang X, Yuan J, Li F. ACD-containing chaperones reveal the divergent thermo-tolerance in penaeid shrimp. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163239. [PMID: 37023801 DOI: 10.1016/j.scitotenv.2023.163239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
The α-crystallin domain-containing (ACD-containing) gene family, which includes typical small heat shock proteins (sHSPs), is the most ubiquitous and diverse family of putative chaperones in all organisms, including eukaryotes and prokaryotes. In the present study, approximately 54-117 ACD-containing genes were identified in five penaeid shrimp species, yielding a significant expansion in comparison with other crustaceans (generally 6-20 ACD-containing genes). Unlike typical sHSPs, which contain a single ACD domain, the ACD-containing genes of penaeid shrimp contain additional ACD domains (3-7 domains, in general), thus having a larger molecular weight and a more complex 3D structure. As indicated by the RNA-seq and qRT-PCR results, the ACD-containing genes of penaeid shrimp showed a strong response to high temperatures. Furthermore, heterologous expression and citrate synthase assays of three representative ACD-containing genes confirmed that their chaperone activity could enhance the thermo-tolerance of E. coli and prevent the aggregation of substrate proteins at high temperatures. Compared with penaeid shrimp species with a relatively low thermo-tolerance (Fenneropenaeus chinensis and Marsupenaeus japonicus), the species with high thermo-tolerance (Litopenaeus vannamei and Fenneropenaeus indicus) contained more ACD-containing genes due to tandem duplication and exhibited biased expression levels under high temperatures. This can explain the divergent thermo-tolerance of different penaeid shrimp species. In conclusion, the ACD-containing genes in penaeid shrimp could be assigned as new chaperones and contribute to their divergent thermo-tolerance phenotypes and adaptations to the ecological environment.
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Affiliation(s)
- Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiaojun Zhang
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianbo Yuan
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fuhua Li
- Chinese Academy of Sciences (CAS) and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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Vinay TN, Patil PK, Aravind R, Anand PSS, Baskaran V, Balasubramanian CP. Microbial community composition associated with early developmental stages of the Indian white shrimp, Penaeus indicus. Mol Genet Genomics 2022; 297:495-505. [PMID: 35129686 DOI: 10.1007/s00438-022-01865-7] [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: 09/08/2021] [Accepted: 01/24/2022] [Indexed: 10/19/2022]
Abstract
Gut microbiota is known to influence the physiology, health, nutrient absorption, reproduction, and other metabolic activities of aquatic organisms. Microbial composition can influence intestinal immunity and are considered as health indicators. Information on gut microbial composition provides potential application possibilities to improve shrimp health and production. In the absence of such information for Penaeus indicus, the present study reports the microbial community structure associated with its early developmental stages. Bacterial community associated with the early developmental stages (egg, nauplii, zoea, mysis, PL1, PL6 and PL12) from two hatchery cycles were analysed employing 16S rRNA high throughput sequencing. Proteobacteria and Bacteroidetes, were the two dominant phyla in P. indicus development stages. Sequential sampling revealed the constant change in the bacterial composition at genus level. Alteromonas was dominant in egg and nauplii stage, whilst Ascidiaceihabitans (formerly Roseobacter) was the dominant genera in both PL6 and PL12. The bacterial composition was highly dynamic in early stages and our study suggests that the mysis stage is the critical phase in transforming the microbial composition and it gets stabilised by early post larval stages. This is the first report on the composition of microbiota in early developmental stages of P. indicus. Based on these results the formation of microbial composition seems to be influenced by feeding at early stages. The study provides valuable information to device intervention strategies for healthy seed production.
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Affiliation(s)
- T N Vinay
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India.
| | - P K Patil
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - R Aravind
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - P S Shyne Anand
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - V Baskaran
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - C P Balasubramanian
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
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Patil PK, Vinay TN, Ghate SD, Baskaran V, Avunje S. 16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus). Antonie van Leeuwenhoek 2021; 114:2019-2031. [PMID: 34536184 DOI: 10.1007/s10482-021-01658-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023]
Abstract
The endemic Indian white shrimp (Penaeus indicus) is an economically important crustacean species, distributed in the Indo-West Pacific region. Knowledge of its gut microbial composition helps in dietary interventions to ensure improved health and production. Here we analyzed V3-V4 hypervariable regions of the 16 S rRNA gene to examine intestinal microbiota in wild and domesticated farmed P. indicus. The study revealed that Proteobacteria, Fusobacteria, Tenericutes, and Bacteroidetes, were the dominant phyla in both the groups although there were differences in relative abundance. The dominant genera in case of the wild group were Photobacterium (29.5 %) followed by Propionigenium (13.9 %), Hypnocyclicus (13.7 %) and Vibrio (11.1 %); while Vibrio (46.5 %), Catenococcus (14 %), Propionigenium (10.3 %) and Photobacterium (8.7 %) were dominant in the farmed group. The results of the study suggest the role of environment on the relative abundance of gut bacteria. This is the first report characterizing gut microbial diversity in P. indicus, which can be used to understand the role of gut microbiota in health, nutrition, reproduction, and growth.
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Affiliation(s)
- Prasanna Kumar Patil
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | | | - Sudeep Darbhe Ghate
- Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Mangalore, India
| | - Viswanathan Baskaran
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - Satheesha Avunje
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
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Huang CW, Chu PY, Wu YF, Chan WR, Wang YH. Identification of Functional SSR Markers in Freshwater Ornamental Shrimps Neocaridina denticulata Using Transcriptome Sequencing. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:772-785. [PMID: 32529453 DOI: 10.1007/s10126-020-09979-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
The amazing colors and patterns are fascinating characteristics in all of the aquarium species. However, genetic and breeding molecular investigations of ornamental shrimps are rather limited. Here, we present the first transcriptomic analysis and application of microsatellites based on the chromatophore-encoded genes of Neocaridina denticulata to assist freshwater ornamental shrimp germplasm enhancement and its extensive applications. A total of 65,402 unigenes were annotated, and 4706 differentially expressed genes were screened and identified between super red shrimp and chocolate shrimp strains. Several gene ratios were examined to put in perspective possible genetic markers for the different strains of normal pigmentation development, including flotillin-2-like, keratin, the G protein-coupled receptor Mth2-like, annexin A7, and unconventional myosin-IXb-like. Five simple sequence repeat markers were effective for colored shrimps and were used to develop a marker-assisted selection platform for systematic breeding management program to maintain genetic diversity of the species. These markers could also be used to assist the identification of pure strains and increase the genetic stability of ornamental shrimp color phenotypes. Consequently, our results of microsatellite marker development are valuable for assisting shrimp genetic and selection breeding studies on freshwater ornamental shrimp and related crystal shrimp species.
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Affiliation(s)
- Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Yu-Fang Wu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Wei-Ren Chan
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City, 20224, Taiwan
| | - Yeh-Hao Wang
- Larmax International Co., Ltd. No.9, Yuanxi 2nd Rd., Changzhi, Pingtung, Taiwan
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Vance DJ, Rothlisberg PC. The biology and ecology of the banana prawns: Penaeus merguiensis de Man and P. indicus H. Milne Edwards. ADVANCES IN MARINE BIOLOGY 2020; 86:1-139. [PMID: 32600543 DOI: 10.1016/bs.amb.2020.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The two banana prawns Penaeus merguiensis and P. indicus are arguably the most commercially important species of penaeid prawns in the tropical and sub-tropical Indo-West Pacific region. They are fecund, short-lived, and have a complex life history involving offshore spawning, inshore mangrove-lined nursery grounds, and migrations between the two locations. We have reviewed and assessed published research on: the fisheries and aquaculture; taxonomy and identification; distribution and habitat preferences; growth; mortality; food and feeding; predation, and the importance of the mangrove habitat to banana prawns. We have examined the life history patterns of these two banana prawns and the many environmental and biological factors that affect different life history stages, often resulting in large interannual variations in abundances of adult prawns and commercial catches. We have also reviewed research on the ecosystem relationships involving these prawns, including fishery impacts on the environment and other species caught as bycatch. In reviewing the published information on factors affecting recruitment dynamics and variability, we have sometimes found contrasting and confounding results, suggesting that these factors are not yet fully understood. Therefore, for each aspect of the prawns' biology we have pointed to areas with incomplete or conflicted understanding, which will hopefully guide future research on these extremely valuable prawn species.
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Affiliation(s)
- David J Vance
- CSIRO Oceans & Atmosphere, Queensland BioSciences Precinct, St Lucia, QLD, Australia.
| | - Peter C Rothlisberg
- CSIRO Oceans & Atmosphere, Queensland BioSciences Precinct, St Lucia, QLD, Australia
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