B. Sahu, Rakesh Kumar Dalai, T. K. Barik, Amiya Kumar Patel
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.
{"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":null,"pages":null},"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}
Shenna Kate M. Torres, Verinna Charisse B. Mangonon, Maria Theresa T. Tengco, Brian S. Santos
The giant trevally (Caranx ignobilis) is an important food fish that faces increasing demand due to human population growth, necessitating genetic monitoring. This study intends to spearhead the development of microsatellite markers to assess the genetic variation of C. ignobilis populations. A total of 150 C. ignobilis specimens from six localities in the Philippines were analyzed. Based on next-generation sequencing data, 12 primer pairs were developed with high amplification rates and polymorphism across different loci. This study introduces the first microsatellite markers exclusively for C. ignobilis, which can be used for monitoring and management purposes.
{"title":"Development and Characterization of 12 Microsatellite Markers for an Economically Important Fish, Caranx ignobilis, in the Philippines","authors":"Shenna Kate M. Torres, Verinna Charisse B. Mangonon, Maria Theresa T. Tengco, Brian S. Santos","doi":"10.4194/ga717","DOIUrl":"https://doi.org/10.4194/ga717","url":null,"abstract":"The giant trevally (Caranx ignobilis) is an important food fish that faces increasing demand due to human population growth, necessitating genetic monitoring. This study intends to spearhead the development of microsatellite markers to assess the genetic variation of C. ignobilis populations. A total of 150 C. ignobilis specimens from six localities in the Philippines were analyzed. Based on next-generation sequencing data, 12 primer pairs were developed with high amplification rates and polymorphism across different loci. This study introduces the first microsatellite markers exclusively for C. ignobilis, which can be used for monitoring and management purposes.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140441527","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}
Rownok Ara Afrin, I. Hoshan, R. Pervin, Nipa Gupta, Md. Nasir Khan, Md. Ashraful Alam, Sharmin Ahmed, Md. Rabiul Awal, I. Parvez
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.
线粒体基因细胞色素 C 氧化酶亚单位 I（mtCOI）已成为研究不同鱼类遗传变异和系统发育关系的一项前景广阔的技术。本研究首次报道了通过分析 mtCOI 基因研究孟加拉国两种外来中国鲤鱼（鲢鱼和鳙鱼）遗传状况的实例。测序结果表明，孟加拉鳙鱼N3和印度鳙鱼M3的核苷酸序列差异最大（1.208），孟加拉鳙鱼N1和印度鳙鱼M3的核苷酸序列差异最小（0.002）。系统进化树分析表明，其中一个 H. nobilis（H. nobilis N3）与 H. molitrix M2 组成姊妹群，序列相似度达 100%。此外，所有测序和参考的 H. molitrix 和 H. nobilis 在系统树中均为独立支系。因此，我们可以得出结论，外来的H. molitrix和H. nobilis保持着不同的种群状态，遗传变异较低。不过，我们今后应采取必要措施减少近亲繁殖。
{"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":null,"pages":null},"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}
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.
珍珠鲻鱼(Alburnus tarichi, g ldenstadt 1814)是一种重要的世界特有鱼类。这一物种是该地区重要的经济和文化资源，因为它生活在世界上最大的湖泊之一的凡湖。根据形态特征来确定鱼的性别通常是不可能的。本研究采用基于地标的几何形态计量学方法对凡湖珍珠鲻鱼种的雌雄形态差异进行了鉴定。以100尾珍珠鲻鱼(雌雄各50尾)为试验材料。在男性和女性之间发现了显著的形态学差异(典型方差分析P<0.001)。这些差异表现为雄鱼的侧面比雌鱼长，雄鱼的头部比雌鱼大。此外，在线框图中，雌性鱼向腹侧形成了一条较深的腹线。位于头部的大鳃的存在是区分雌鱼和雄鱼的另一个重要特征。两性之间的侧体和腹体差异通过方差分析(ANOVA)检验结果进行统计。
{"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":null,"pages":null},"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}
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.
{"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":null,"pages":null},"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}
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.
{"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":null,"pages":null},"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}
J. Gerszon, Berit Genz, L. Franz, M. Sellars, R. Moser
Selecting the appropriate lysis buffers is crucial in obtaining high-quality nucleic acids for molecular pathogen detection. In this study, we compared three in-house and one commercial lysis buffer for their effectiveness in extracting high-quality TNA from Tiger shrimp and sandworm samples. Buffer L1 outperformed the commercial counterpart, producing higher TNA concentrations and concordant PCR results for all DNA and RNA targets in the Shrimp MultiPathTM. The findings underscore the significance of selecting the right extraction buffers to achieve high-quality nucleic acids for downstream molecular applications and suggest that in-house buffers can be a viable alternative to commercial ones for difficult-to-extract tissues.
{"title":"Comparative Evaluation of Custom TNA Extraction Buffers to Obtain High-quality TNA from Shrimp and Polychaetes","authors":"J. Gerszon, Berit Genz, L. Franz, M. Sellars, R. Moser","doi":"10.4194/ga572","DOIUrl":"https://doi.org/10.4194/ga572","url":null,"abstract":"Selecting the appropriate lysis buffers is crucial in obtaining high-quality nucleic acids for molecular pathogen detection. In this study, we compared three in-house and one commercial lysis buffer for their effectiveness in extracting high-quality TNA from Tiger shrimp and sandworm samples. Buffer L1 outperformed the commercial counterpart, producing higher TNA concentrations and concordant PCR results for all DNA and RNA targets in the Shrimp MultiPathTM. The findings underscore the significance of selecting the right extraction buffers to achieve high-quality nucleic acids for downstream molecular applications and suggest that in-house buffers can be a viable alternative to commercial ones for difficult-to-extract tissues.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42521444","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}
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.
{"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":null,"pages":null},"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}
L. P. Cheriyan, M. Oommen, Sanil George, Anoop VasudevanSheeja
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.
{"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":null,"pages":null},"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}
Sk Injamamul Islam, Saloa Sanjida, Md Akib Ferdous, Nasim Habib
This study used a comprehensive bioinformatic application to discover the functions of the HP33 protein, which is responsible for the scale drop and muscle necrosis disease (SDMND) in fish. The main objective of the study was to the characterization of the HP33 protein and predict the homo-oligomer models to understand the physical effect of the protein for further research. At first, multiple sequence alignment and sub-cellular localization of the HP33 were predicted by the in-silico approach. The result suggests that this putative protein clustered with another hypothetical protein, Vibrio harveyi, and is an unstable, nonpolar, and outer membrane protein. Functional analysis of the protein by Pfam, InterProScan, and SMART tools predicts that the HP has a single functional domain that may signify a cluster of biosynthetic genes. The prediction of the active site, as well as the protein-protein interaction, were also predicted in this study. Furthermore, a protein-ligand docking investigation revealed two potential therapeutic compounds (Ferroheme C, Valine) that can be effective against HP33 pathogenesis. In conclusion, the homo-oligomers model's predictions and the ab-initio docking findings will offer important information for an additional immunological investigation, which may be beneficial in a future study on SDMND prophylaxis.
{"title":"Synthesis of Homo-oligomer Models, Functional Characterization, and Annotation of the Virulent HP33 Protein from the Vibrio harveyi Strain of Scale Drop and Muscle Necrosis Disease","authors":"Sk Injamamul Islam, Saloa Sanjida, Md Akib Ferdous, Nasim Habib","doi":"10.4194/ga550","DOIUrl":"https://doi.org/10.4194/ga550","url":null,"abstract":"This study used a comprehensive bioinformatic application to discover the functions of the HP33 protein, which is responsible for the scale drop and muscle necrosis disease (SDMND) in fish. The main objective of the study was to the characterization of the HP33 protein and predict the homo-oligomer models to understand the physical effect of the protein for further research. At first, multiple sequence alignment and sub-cellular localization of the HP33 were predicted by the in-silico approach. The result suggests that this putative protein clustered with another hypothetical protein, Vibrio harveyi, and is an unstable, nonpolar, and outer membrane protein. Functional analysis of the protein by Pfam, InterProScan, and SMART tools predicts that the HP has a single functional domain that may signify a cluster of biosynthetic genes. The prediction of the active site, as well as the protein-protein interaction, were also predicted in this study. Furthermore, a protein-ligand docking investigation revealed two potential therapeutic compounds (Ferroheme C, Valine) that can be effective against HP33 pathogenesis. In conclusion, the homo-oligomers model's predictions and the ab-initio docking findings will offer important information for an additional immunological investigation, which may be beneficial in a future study on SDMND prophylaxis.","PeriodicalId":36569,"journal":{"name":"Genetics of Aquatic Organisms","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48108546","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}
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