Genetics of Aquatic Organisms最新文献

Advances in Transcriptomic Technologies and Their Applications in Fisheries Science 转录组学技术及其在渔业科学中的应用进展

Genetics of Aquatic Organisms Pub Date : 2025-08-29 DOI: 10.4194/ga882

Amit Pande, Raja Aadil Hussain Bhat, Yamini Lohumi, Ankita H. Tripathi, Santosh K. Upadhyay

{"title":"Advances in Transcriptomic Technologies and Their Applications in Fisheries Science","authors":"Amit Pande, Raja Aadil Hussain Bhat, Yamini Lohumi, Ankita H. Tripathi, Santosh K. Upadhyay","doi":"10.4194/ga882","DOIUrl":"https://doi.org/10.4194/ga882","url":null,"abstract":"Transcriptomics is the study of the entire set of RNA transcripts within a cell. It provides insights into the active and latent processes occurring at the subcellular level. Since its inception in the early nineties, it has revolutionized molecular biology and related fields. It has helped uncover the connections between genes and pathways, as well as their roles in physiology, biochemical processes, and disease. Advances in sequencing technologies have further resolved the complexity of cellular functions and provided a snapshot of the transcripts present in a cell at a given time. Over the past decade, transcriptomics has been extensively applied in aquaculture to identify and characterize transcripts associated with immune responses and physiological pathways. This approach allows researchers to study how transcript levels change across organisms, tissues, and cells in response to different stimuli, and thus permits the detection of broadly coordinated mechanisms. More recently, single-cell-based multi-omics techniques have revolutionized biological research. Although their application in fisheries science is still limited; however, it has enormous potential to address many unanswered research problems in this area. In this review, a broad idea about transcriptomics has been given with emphasis on single-cell isolation techniques and the available sequencing domain of single-cell omics. Additionally, we attempt to highlight a few of the important applications of single-cell and multi-cell transcriptomics in fisheries science.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"9 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://doi.org/10.4194/ga882","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147911016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular Insights into the Identification, Diversity and Phylogenetics of the Por`s Goatfish Upeneus pori (Actinopterygii: Syngnathiformes: Mullidae) from Odisha Coast, Bay of Bengal, India 对印度孟加拉湾奥迪沙海岸的山羊鱼 Upeneus pori（翼手目：鞘形目：鲻科）的鉴定、多样性和系统发育的分子见解

Genetics of Aquatic Organisms Pub Date : 2024-07-19 DOI: 10.4194/ga770

B. Sahu, Rakesh Kumar Dalai, T. K. Barik, Amiya Kumar Patel

{"title":"Molecular Insights into the Identification, Diversity and Phylogenetics of the Por`s Goatfish Upeneus pori (Actinopterygii: Syngnathiformes: Mullidae) from Odisha Coast, Bay of Bengal, India","authors":"B. Sahu, Rakesh Kumar Dalai, T. K. Barik, Amiya Kumar Patel","doi":"10.4194/ga770","DOIUrl":"https://doi.org/10.4194/ga770","url":null,"abstract":"Numerous different habitats found in marine environments are often conducive to migration and ecological adaption of various marine organisms. The inherent drawbacks of morphology-based identification systems have made it imperative to develop trustworthy genetic techniques that permit the unambiguous identification of fish species. In the present study, seven specimens of the goatfish Upeneus pori Ben-Tuvia and Golani, 1989, were recorded (February 2021) for the first time from the Odisha coast, Bay of Bengal, India. Their DNA was isolated, and mtCOI barcode regions of four specimens were amplified and sequenced successfully. The generated barcode sequences were analyzed using different molecular approaches. U. pori exhibited low genetic variation within populations (average K2P distance = 0.0046). The median joining network of U. pori was simple, with only five haplotypes, including one haplotype present in this region. The analysis of the variation of the amino acids in the mtCOI barcode sequences suggested that there were no significant variations found among U. pori of different geographical locations. The species U. pori was diverged from its common ancestor during the late Miocene sub-epoch, which was around 6.38 Mya. These findings provide insights into the population genetics and evolutionary history of U. pori in this region.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"121 31","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141820902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and Characterization of 12 Microsatellite Markers for an Economically Important Fish, Caranx ignobilis, in the Philippines 菲律宾一种具有重要经济价值的鱼类 Caranx ignobilis 的 12 个微卫星标记的开发和特征描述

Genetics of Aquatic Organisms Pub Date : 2024-02-22 DOI: 10.4194/ga717

Shenna Kate M. Torres, Verinna Charisse B. Mangonon, Maria Theresa T. Tengco, Brian S. Santos

引用次数: 0

Genetic Status of Exotic Chinese Carp Hypophthalmichthys molitrix and Hypophthalmichthys nobilis through Mitochondrial Gene Cytochrome C Oxidase Subunit I (COI) in Bangladesh 通过线粒体基因细胞色素 C 氧化酶亚单位 I (COI) 分析孟加拉国外来鲤鱼 Hypophthalmichthys molitrix 和 Hypophthalmichthys nobilis 的遗传状况

Genetics of Aquatic Organisms Pub Date : 2024-01-24 DOI: 10.4194/ga668

Rownok Ara Afrin, I. Hoshan, R. Pervin, Nipa Gupta, Md. Nasir Khan, Md. Ashraful Alam, Sharmin Ahmed, Md. Rabiul Awal, I. Parvez

{"title":"Genetic Status of Exotic Chinese Carp Hypophthalmichthys molitrix and Hypophthalmichthys nobilis through Mitochondrial Gene Cytochrome C Oxidase Subunit I (COI) in Bangladesh","authors":"Rownok Ara Afrin, I. Hoshan, R. Pervin, Nipa Gupta, Md. Nasir Khan, Md. Ashraful Alam, Sharmin Ahmed, Md. Rabiul Awal, I. Parvez","doi":"10.4194/ga668","DOIUrl":"https://doi.org/10.4194/ga668","url":null,"abstract":"The use of mitochondrial gene Cytochrome C Oxidase subunit I (mtCOI) has emerged as a promising technique in study of genetic variation and phylogenetic relationship of different group of fishes. This work reports the first example of the study of genetic status of two exotic Chinese carp, silver carp, Hypophthalmichthys molitrix and bighead carp, Hypophthalmichthys nobilis in Bangladesh through the analyses of mtCOI gene. The highest nucleotide sequence divergence occurred between sequenced H. nobilis N3 and reference H. molitrix from India which was 1.208 and the lowest nucleotide divergence occurred in sequenced H. nobilis N1 and sequenced H. molitrix M3 with their reference counterparts from Bangladesh, India and China (0.002). The phylogenetic tree analysis showed that one of the H. nobilis (H. nobilis N3) formed a sister group with H. molitrix M2 with 100% sequence similarities. Otherwise, all sequenced and reference H. molitrix and H. nobilis showed separate clade in the tree. Therefore, we can conclude that the exotic H. molitrix and H. nobilis maintain distinct population status with lower genetic variation. However, we should take essential measures to reduce inbreeding in future.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"8 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140497178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gender Determination of Pearl Mullet by Geometric Morphometric Method 几何形态计量法测定珍珠鲻性别

Genetics of Aquatic Organisms Pub Date : 2023-09-13 DOI: 10.4194/ga603

Veysel Delibas, Zafer Soyguder, Gamze Cakmak

{"title":"Gender Determination of Pearl Mullet by Geometric Morphometric Method","authors":"Veysel Delibas, Zafer Soyguder, Gamze Cakmak","doi":"10.4194/ga603","DOIUrl":"https://doi.org/10.4194/ga603","url":null,"abstract":"Pearl mullet (Alburnus tarichi, Güldenstadt 1814) is an endemic fish species of great importance worldwide. This species is an important economic and cultural resource for the region since it lives in Lake Van, one of the world's largest sodic lakes. It is often not possible to determine the sex of fish based on morphological characteristics. In this study, landmark-based geometric and morphometric method was preferred to identify the shape difference between male and female sexes of pearl mullet fishes species in Lake Van. A total of 100 pearl mullet fish (50 females and 50 males) were used as material. Significant morphological differences were found between the male and female sexes (P<0.001 in canonical analysis of variance). These differences were found that the male fishes were longer than the female fishes on the lateral side and the head of the male fishes were larger than the female fishes. In addition, female fishes formed a deeper abdominal line towards the ventral side in the wireframe graph. The presence of a large gill positioned cranially is another important feature that distinguishes female fishes from male fishes. Lateral and ventral body differences between the sexes were statistically determined by ANOVA test results.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"40 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135785714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Characterizing the Dark Mahseer, Naziritor chelynoides (McClelland, 1839): A Morphological, Osteological, and Molecular Approach 表征暗马舍尔，Naziritor chelynoides (McClelland, 1839):形态学，骨学和分子方法

Genetics of Aquatic Organisms Pub Date : 2023-08-03 DOI: 10.4194/ga601

Neetu Shahi, Debajit Sarma, Bhupendra Singh, Sumanta Kumar Mallik, Deepjyoti Baruah, Ravindra Posti, Radheshyam Haldar, Irengbam Linthoingambi

{"title":"Characterizing the Dark Mahseer, Naziritor chelynoides (McClelland, 1839): A Morphological, Osteological, and Molecular Approach","authors":"Neetu Shahi, Debajit Sarma, Bhupendra Singh, Sumanta Kumar Mallik, Deepjyoti Baruah, Ravindra Posti, Radheshyam Haldar, Irengbam Linthoingambi","doi":"10.4194/ga601","DOIUrl":"https://doi.org/10.4194/ga601","url":null,"abstract":"Dark mahseer, Naziritor chelynoides is a vulnerable stream fish in several Asian countries, and developing an effective conservation strategy is impeded by incomplete information about its taxonomy. To address this research gap, in the current study dark mahseer collected from Himalayan stream in India (29°21`99.5` N and 79°33`23.9` E) were examined for their morphometric, meristic, osteological, and molecular characteristics. This study discovered unique features of dark mahseer, including its thin non-hypertrophied lower lip without median lobe, complete post-labial groove, 33 to 34 central perforated lateral line scales, a dark elliptical blotch at the angle of the operculum, and numerous fine black dots on a crescent pattern on scales. This species has 9 to 11 slender gill rakers (595.93±148.71 μm in length), 40 to 41 total vertebrae, 38 to 39 neural spines, 14 to 15 hemal spines, and fused first to fourth abdominal vertebrae. Molecular analysis of cytochrome c oxidase subunit 1 gene (cox1), cytochrome b (cytb), and ATPase subunit 6&8 (ATPase 6&8) genes revealed the genetic distance of 0.08 to 0.10, 0.12 to 0.13, and 0.01 to 0.11 respectively from other Tor species. Our study enhances knowledge of dark mahseer's taxonomy, supporting conservation strategies for this valuable fish species.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"89 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136382286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genus-specific Primer Design for Molecular Identification of Rhodobacter sp. Origin of the 16S rRNA Gene Rhodobacter sp.分子鉴定属特异性引物设计。16S rRNA基因的来源

Genetics of Aquatic Organisms Pub Date : 2023-06-23 DOI: 10.4194/ga588

Rifky Rizkiantino, Rubiyanto Widodo Haliman, Beni Halalludin, Yuri Sutanto, Rachmawati Nur Fitriana, Bestran Virlando Panjaitan, Putri Purnama Sari, Mufti Rahayu, Hendi Yanto Efendy, Hendri Laiman

{"title":"Genus-specific Primer Design for Molecular Identification of Rhodobacter sp. Origin of the 16S rRNA Gene","authors":"Rifky Rizkiantino, Rubiyanto Widodo Haliman, Beni Halalludin, Yuri Sutanto, Rachmawati Nur Fitriana, Bestran Virlando Panjaitan, Putri Purnama Sari, Mufti Rahayu, Hendi Yanto Efendy, Hendri Laiman","doi":"10.4194/ga588","DOIUrl":"https://doi.org/10.4194/ga588","url":null,"abstract":"Rhodobacter is one of the purple phototropic bacteria widely used in aquaculture activity. It is particularly difficult in identifying and distinguishing Rhodobacter from other non-sulfur purple bacteria. This study aimed to evaluate primer pairs designed based on the 16S rRNA gene from Rhodobacter as an effective and efficient molecular identification that can be performed in the laboratory using conventional PCR techniques. The 16S rRNA sequences from Rhodobacter and other bacteria were aligned and analyzed for the high-variation region to capture the desired target amplicon. Forward and reverse primer pairs were designed based on the appropriate target amplicon. The primer pairs were also assessed for their feasibility based on ten assessment criteria for the quality of the PCR primers. The PCR optimization results obtained showed a specific band with a size of 548 bp according to the amplicon target size in the Rhodobacter samples tested and did not show any cross-reaction with other comparator bacteria, and no dimers or other non-specific bands were found. Based on the results obtained, it can be concluded that the primer pairs designed in terms of quality and specificity are good and can be used as alternative specific primers for the genus Rhodobacter sp.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136084394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative Evaluation of Custom TNA Extraction Buffers to Obtain High-quality TNA from Shrimp and Polychaetes 从虾和多血细胞中获得高质量TNA的定制TNA提取缓冲液的比较评价

Genetics of Aquatic Organisms Pub Date : 2023-04-03 DOI: 10.4194/ga572

J. Gerszon, Berit Genz, L. Franz, M. Sellars, R. Moser

引用次数: 0

Analysis of Partial Mitochondrial COI and 16S rRNA Gene Sequences Variation of Pagurus brachiomastus and Pagurus proximus (Decapoda: Paguridae) Populations from the South of Russian Far East 俄罗斯远东南部地区腕足田鼠和近端田鼠(十足目:田鼠科)部分线粒体COI和16S rRNA基因序列变异分析

Genetics of Aquatic Organisms Pub Date : 2023-02-28 DOI: 10.4194/ga574

D. Atopkin

{"title":"Analysis of Partial Mitochondrial COI and 16S rRNA Gene Sequences Variation of Pagurus brachiomastus and Pagurus proximus (Decapoda: Paguridae) Populations from the South of Russian Far East","authors":"D. Atopkin","doi":"10.4194/ga574","DOIUrl":"https://doi.org/10.4194/ga574","url":null,"abstract":"Mitochondrial COI and 16S rRNA gene partial sequences were generated for Pagurus brachiomastus from two locations and P. proximus from single location of the south of Russian Far East. Genetic variation and differentiation of P. brachiomastus Russian and South Korean (GenBank data) populations were estimated and compared on the basis of sequence data on two mitochondrial genes separately. Additionally, P. simulans from South Korea was analyzed. Results show P. brachiomastus from two locations of the south of Russian Far East and South Korea and Korean P. simulans differs at intraspecific level based on molecular markers. Median-Joining analysis indicate presence of two main groups of haplotypes, representing P. proximus and P. brachiomastus + P. simulans, respectively. These data support that P. brachiomastus and P. simulans are conspecific. Mismatch distribution analysis showed population growth for P. brachiomastus at the south of Russian Far East. Sequence pairwise variations of both molecular markers appear differently in two far eastern samples of P. brachiomastus, that can be partially explained by active gene flow through hermit crab migrations between two localities after their isolation.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46942482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Pilot Study on The Population Genetic Structure of the Selected Fish Species from Meenachil River, India 印度Meenachil河选定鱼类种群遗传结构的初步研究

Genetics of Aquatic Organisms Pub Date : 2023-02-03 DOI: 10.4194/ga543

L. P. Cheriyan, M. Oommen, Sanil George, Anoop VasudevanSheeja

{"title":"A Pilot Study on The Population Genetic Structure of the Selected Fish Species from Meenachil River, India","authors":"L. P. Cheriyan, M. Oommen, Sanil George, Anoop VasudevanSheeja","doi":"10.4194/ga543","DOIUrl":"https://doi.org/10.4194/ga543","url":null,"abstract":"Meenachil River is the only river originating from Southern Western Ghats of India having human settlement right from the headwaters to the mouth. The river is subjected to human-induced stressors to varying extents, resulting in a drastic decline in riverine health and fish diversity. The population genetic structure of two species commonly distributed in different geographical zones of Meenachil River, Dawkinsia filamentosa and Pseudetroplus maculatus were studied using the 16S mitochondrial ribosomal RNA gene sequences. Haplotype clustering and the presence of unique haplotypes were identified by phylogenetic and network analysis. Six haplotypes were identified for D. filamentosa and ten for P. maculatus. The neutrality estimations of the upstream and midstream populations of the species revealed the presence of an excess of common alleles with neutral mutations indicating a population expansion after bottleneck and stabilizing selection. The downstream population revealed the presence of an excess of rare alleles with non-neutral mutations indicating a positive directional selection and population sub-division. Population expansion demonstrated star-like phylogenies with rare haplotypes separated by mutational steps from the ancestral haplotypes. The private haplotypes indicated the existence of selection pressure in the downstream zone of the river.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43152219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0