scholarly journals Genetic diversity of blue swimming crab (Portunus pelagicus Linn 1758) from Indonesian waters (Sunda and Sahul Shelf, Wallacea region): Phylogenetic approach

2020 ◽  
Vol 21 (5) ◽  
Author(s):  
Andi Aliah Hidayani ◽  
Yushinta Fujaya ◽  
Dody Dharmawan Trijuno ◽  
Nita Rukminasari ◽  
Alimuddin Alimuddin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Swimming Crab ◽  
Sunda Shelf ◽  
Unique Haplotype ◽  
High Genetic Diversity ◽  
Portunus Pelagicus ◽  
South Sulawesi ◽  
Study Sites ◽  
Swimming Crabs

Abstract. Hidayani AA, Fujaya Y, Trijuno DD, Rukminasari N, Alimuddin A. 2020. Genetic diversity of blue swimming crab (Portunus pelagicus Linnaeus 1758) from Indonesian waters (Sunda and Sahul Shelf, Wallacea region): Phylogenetic approach. Biodiversitas 21: 2097-2102. Blue swimming crab is one of the exploited fisheries commodities in Indonesia. This condition has contributed to the decline of their genetic diversity. The information on genetic diversity assumes importance for the conservation and the cultural purposes of species. The study aimed to determine the genetic diversity of blue swimming crabs from Indonesian waters using phylogenetic analysis. We conducted sampling of crab from several Indonesian waters, such the Aceh and Semarang (representing Sunda Shelf), Barru, South Sulawesi, and Maumere, Flores (representing Wallacea region) and Sorong, Raja Ampat and Kaimana (representing Sahul Shelf). Genetic diversity in this study using mitochondrial DNA (mtDNA) by implementing the method of Cytochrome c Oxidase Subunit I (COI). According to the findings, the blue swimming crabs from our study sites had a high genetic diversity variation. Three groups of crabs were determined using phylogenetic tree which formed three different unique clades. There was the same haplotype of crab observed from different locations, barring a sample from the Sahul Shelf which has a unique haplotype. There was no genetic speciation of crab samples from the Sunda Shelf and the Wallacea region were observed, except samples from the Sahul Shelf. Hybridization might occur between species of the crabs due to the finding of a cryptic species. 

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

scholarly journals Gonad maturity and gonadal somatic index of blue swimming crab Portunus pelagicus harvested from Spermonde Archipelago, South Sulawesi, Indonesia

2021 ◽  
Vol 6 (1) ◽  
pp. 23-26
Author(s):  
Muh. Saleh Nurdin ◽  
Fauziah Azmi ◽  
Teuku Fadlon Haser
Keyword(s):  
Coral Reef ◽  
Reproductive Biology ◽  
Maturity Stage ◽  
Swimming Crab ◽  
Portunus Pelagicus ◽  
Gonad Maturity ◽  
South Sulawesi ◽  
Coral Reef Ecosystems ◽  
Gonadal Somatic Index ◽  
Spermonde Archipelago

Reproductive biology is one of the biological aspects that needed to formulate responsible management of blue swimming crab (BSC). The crab is one of the commercial fisheries commodities in South Sulawesi, Indonesia. Presently no information on the reproductive biology of this crab from Spermonde Archipelago, Sout Sulawesi. Therefore, the study aimed to analyze and compare gonad maturity stage(GMS)andgonadalsomaticindex(GSI)oftheBSCcaughtonthreeecosystemsnamelycoralreef,seagrass,andmangrovein Salemo Island, Spermonde Archipelago. GMS and GSI were analyzed descriptively for five months from March to July 2015. Results indicate there was a difference in GMS of the BSC caught in mangroves, seagrass, and coral reef. Generally, mangrove was dominated by immature BSC with GMS I and GMS II, while the BSC caught in the seagrass and coral reef BSC were dominantly mature and spawn GMS III, IV, and V. GSI BSC caught in mangrove ecosystem are smaller than GSI BSC caught in seagrass and coral reef ecosystems. Seagrass and coral reef ecosystems suitable for development no-take zone of the BSC.

scholarly journals VARIABILITY OF CARAPACE WIDTH SIZE AND ABUNDANCE OF BLUE SWIMMING CRABS (Portunus pelagicus Linnaeus) IN PATI WATERS

2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Dyah Ika Nugraheni ◽  
Achmad Fahrudin ◽  
. Yonvitner
Keyword(s):  
Coastal Waters ◽  
Accretion Rate ◽  
Carapace Width ◽  
Management Strategies ◽  
Fishing Effort ◽  
Swimming Crab ◽  
Nearshore Zone ◽  
Portunus Pelagicus ◽  
Males And Females ◽  
Swimming Crabs

<p><em>Fishing effort enhancement would put pressure on blue swimming crab resources and its ecosystem. The objective of this study was to determine the spatial distribution based on the size of the carapace width (CW), abundance, temperature, salinity, depth, and fishing intensity in Pati waters which was divided into two zones (zones 1=nearshore, zone 2=offshore). The result showed that the average of carapace width in zone 1 to zone 2 was significantly different (p &lt;0.05), as well as between males and females. Average number of individual (abundance) was significantly different according to fishing areas and sex (p &lt;0.05). The average of water temperature in zone 1 was higher than in zone 2, salinity in zone 1 was smaller than in zone 2, and the water depth in zone 1 was shallower than in zone 2. The higher the crab catch intensity leaded to the smaller the abundance and size of carapace width. Alternative management strategies were proposed such as to divert fishing grounds from coastal waters to offshore during low productivity season, to uphold rules on minimum legal size for catching (Lm = 107 mm),  to release of berried females catch, and to reduce accretion rate of gear and fishing fleet mainly in the coastal zone waters.</em></p><p><em><strong><em>Keywords:  </em></strong><em>blue swimming crab, carapace widht (CW), abundance, intensity of fishing</em></em></p>

Genetic diversity ofFrankiastrains in root nodules fromHippophae¨ rhamnoidesL.

Botany ◽  
2008 ◽  
Vol 86 (3) ◽  
pp. 240-247 ◽  
Author(s):  
Li-hong Chen ◽  
Jian Liu ◽  
Gui-min Yao ◽  
Wei Yan
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Restriction Analysis ◽  
Root Nodules ◽  
Plant Cover ◽  
Practical Importance ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Northern China ◽  
High Genetic Diversity

The Hippophae¨ rhamnoides L. – Frankia symbiosis is of ecological and practical importance, but very little is known about H. rhamnoides-infective Frankia strains. To address this problem, we have used PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of nifD–nifK intergenic spacer (IGS) to estimate their genetic diversity at 19 sites in Northern China. Restriction analysis indicated that H. rhamnoides-infective Frankia had a high genetic diversity; the samples were divided into nine RFLP patterns (A–I). Elevation and precipitation likely affect the distribution of different Frankia patterns in root nodules. The patterns A and D were present in relatively large areas, which were located at various elevations; however, the distribution of patterns B, C, E, F, G, H, and I generally followed a geographic range. The richness of Frankia diversity was influenced by plant cover and geographic factors such as elevation and precipitation. H. rhamnoides cover had a higher diversity than that of natural vegetation cover. The center part of the geographical range, with intermediate elevation and precipitation, had a higher level of Frankia diversity than that of the west part and east part with high or low elevations and precipitations, respectively. The nifD–nifK IGS regions were sequenced from 28 nodule samples. Phylogenetic analysis showed that H. rhamnoides-infective Frankia strains were all clustered with the Elaeagnus group, and the diversity of this group was quite extensive. Phylogenetic relationships between Hippophae¨ and Elaeagnus-infective Frankia strains were relatively close to each other. Although not very close to either Hippophae¨- or Elaeagnus-infective Frankia strains, Shepherdia -infective strain SCN10a was closer to Hippophae¨-infective strains than to Elaeagnus- infective strains. This is the first detailed report on the genetic diversity and phylogenetic analysis of H. rhamnoides-infective Frankia.

scholarly journals High genetic diversity of hepatitis delta virus in eastern Turkey

2014 ◽  
Vol 8 (01) ◽  
pp. 074-078 ◽  
Author(s):  
Yasemin Bulut ◽  
Ibrahim Halil Bahcecioglu ◽  
Cem Aygun ◽  
Pinar Demirel Oner ◽  
Ibrahim Ozercan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Restriction Enzyme ◽  
Hepatitis Delta Virus ◽  
Rt Pcr ◽  
Genotype I ◽  
High Genetic Diversity ◽  
Hepatitis Delta ◽  
Hdv Genotype ◽  
Delta Virus

Introduction: Hepatitis delta virus (HDV) is a serious cause of liver-related mortality in patients infected with hepatitis B virus (HBV). Determination of genotypes of HDV and phylogenetic analysis are important for better understanding the pathogenesis of the liver diseases associated with HBV infection. The aim of this study was to determine the genotype or genotypes of HDV among chronically infected patients with HBV in eastern Turkey. Methodology: A group of 113 patients infected with HBV and HDV were included in this study. The samples taken from the patients were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction enzyme cleavage. Results: According to the results of the restriction enzyme analysis, all of the RT-PCR products were determined to be HDV genotype I. Furthermore, for phylogenetic analysis and genotyping, 40 of HDV RT-PCR positive products were sequenced. Phylogenetic analysis of the sequences showed that all of the samples were infected with HDV genotype I. In addition, the results of the alignment analysis showed that the sequences of clinical samples were 82%-95% similar. Conclusion: These results indicate that high genetic diversity of the virus is possible in endemic areas such as Turkey.

scholarly journals Parasite genetic diversity reflects continued residual malaria transmission in Vhembe District, a hotspot in the Limpopo Province of South Africa

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Hazel B. Gwarinda ◽  
Sofonias K. Tessema ◽  
Jaishree Raman ◽  
Bryan Greenhouse ◽  
Lyn-Marié Birkholtz
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Malaria Transmission ◽  
Limpopo Province ◽  
Parasite Population ◽  
High Genetic Diversity ◽  
Management Interventions ◽  
Imported Cases ◽  
Study Sites ◽  
Vhembe District

Abstract Background South Africa aims to eliminate malaria transmission by 2023. However, despite sustained vector control efforts and case management interventions, the Vhembe District remains a malaria transmission hotspot. To better understand Plasmodium falciparum transmission dynamics in the area, this study characterized the genetic diversity of parasites circulating within the Vhembe District. Methods A total of 1153 falciparum-positive rapid diagnostic tests (RDTs) were randomly collected from seven clinics within the district, over three consecutive years (2016, 2017 and 2018) during the wet and dry malaria transmission seasons. Using 26 neutral microsatellite markers, differences in genetic diversity were described using a multiparameter scale of multiplicity of infection (MOI), inbreeding metric (Fws), number of unique alleles (A), expected heterozygosity (He), multilocus linkage disequilibrium (LD) and genetic differentiation, and were associated with temporal and geospatial variances. Results A total of 747 (65%) samples were successfully genotyped. Moderate to high genetic diversity (mean He = 0.74 ± 0.03) was observed in the parasite population. This was ascribed to high allelic richness (mean A = 12.2 ± 1.2). The majority of samples (99%) had unique multi-locus genotypes, indicating high genetic diversity in the sample set. Complex infections were observed in 66% of samples (mean MOI = 2.13 ± 0.04), with 33% of infections showing high within-host diversity as described by the Fws metric. Low, but significant LD (standardised index of association, ISA = 0.08, P < 0.001) was observed that indicates recombination of distinct clones. Limited impact of temporal (FST range − 0.00005 to 0.0003) and spatial (FST = − 0.028 to 0.023) variation on genetic diversity existed during the sampling timeframe and study sites respectively. Conclusions Consistent with the Vhembe District’s classification as a ‘high’ transmission setting within South Africa, P. falciparum diversity in the area was moderate to high and complex. This study showed that genetic diversity within the parasite population reflects the continued residual transmission observed in the Vhembe District. This data can be used as a reference point for the assessment of the effectiveness of on-going interventions over time, the identification of imported cases and/or outbreaks, as well as monitoring for the potential spread of anti-malarial drug resistance.

scholarly journals Kajian Tingkat Kerentanan Rajungan (Portunus pelagicus) di Perairan Desa Tunggulsari Kabupaten Rembang

2021 ◽  
Vol 10 (1) ◽  
pp. 147-157
Author(s):  
Parameswari Iccha Nirmalabuddhi Wishnuputri ◽  
Sri Redjeki ◽  
Retno Hartati
Keyword(s):  
Water Quality ◽  
Growth Pattern ◽  
Economic Value ◽  
Quality Parameters ◽  
Swimming Crab ◽  
Portunus Pelagicus ◽  
Male And Female ◽  
Over Exploitation ◽  
The Village ◽  
Swimming Crabs

Rajungan (Portunus pelagicus) adalah salah satu sumber daya hayati laut Indonesia. Rajungan merupakan komoditas utama  perikanan di Indonesa, baik untuk lokal maupun ekspor. Nilai ekonomis rajungan yang tergolong tinggi mengakibatkan penangkapan rajungan dilakukan secara besar-besar dan dapat memicu terjadinya kepunahan. Penelitian bertujuan untuk mengetahui tingkat kerentanan rajungan di Perairan Desa Tunggulsari dan mengetahui karakteristik morfometri dari rajungan yang ditangkap pada lokasi tersebut. Metode yang digunakan dalam penelitian ini adalah metode Productivity and Susceptibility Analysis (PSA). Wawancara dilakukan kepada 60 nelayan di Desa Tunggulsari. Pengukuran parameter kualitas perairan meliputi suhu, oksigen terlarut, salinitas, dan pH. Pengukuran morfometri dilakukan pada salah satu pengepul di desa. Hasil dari wawancara diketahui bahwa nelayan di Desa Tunggulsari menggunakan 2 macam alat tangkap yaitu bubu lipat dan jaring insang dasar. Penilaian atribut produktivitas rajungan masuk dalam kategori tinggi, sedangkan penilaian atribut kerentanan tergolong pada resiko rendah untuk penggunaan kedua alat tersebut. Nilai MSC untuk alat tangkap bubu lipat adalah 96,0 dan 98,2 untuk alat tangkap jaring insang dasar. Nilai MSC > 80 menunjukkan bahwa tingkat kerentanan rajungan pada lokasi tersebut masuk pada kategori rendah. Selanjutnya, pola pertumbuhan rajungan di Desa Tunggulsari adalah allometrik negatif baik untuk rajungan jantan maupun betina. Hal ini menunjukkan pertumbuhan panjang dan lebar karapas lebih cepat dibandingkan penambahan berat rajungan. The blue swimming crab (Portunus pelagicus) is one of the Indonesian marine biological resources. The blue swimming crab is a main commodity of fisheries in Indonesia, both for local and export. Economic value of blue swimming crab classified as high involve over-exploitation of blue swimming crab and can lead to extinction. This research is aimed to determine level of vulnerability of blue swimming crab in Tunggulsari waters and to discover morphometry characteristic of blue swimming crab that caught at that location. The method used in this research is Productivity and Susceptibility (PSA) method. Interviews were conducted with 6 fishermen in the village of Tunggulsari. Measurement of water quality parameters including temperature, dissolved oxygen, salinity, and pH. Morphometry measurement was carried out in one of the collectors in the village. The results of the interview revealed that fishermen in the village of Tunggulsari used 2 fishing tools namely bubu lipat and bottom set gillnet. Assessment of blue swimming crab productivity attributes is included in the high category, while the assessment of vulnerability attributes is classified as low risk for the use of both tools. The MSC value for bubu lipat is 96,0 and 98,2 for bottom set gillnet. The MSC value is more than 80 indicates that the level of blue swimming crab vulnerability at that location is in the low category. Further, blue swimming crab growth pattern in the village of Tunggulsari are negative allometrics for both male and female blue swimming crabs. This shows the growth in length and width carapace is faster than the addition of blue swimming crab weight.

scholarly journals DETERMINATION OF GENETIC DIVERSITY IN PORTUNUS PELAGICUS (LINNAEUS, 1758) COLLECTED FROM GULF OF MANNAR

2021 ◽  
Vol 9 (03) ◽  
pp. 409-420
Author(s):  
C. Shibana ◽  
◽  
P. Subavathy ◽  
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Gulf Of Mannar ◽  
High Genetic Diversity ◽  
Portunus Pelagicus ◽  
Specific Level ◽  
Main Emphasis ◽  
Geographical Regions ◽  
High Level

In the present study, the marine crab Portunuspelagicus was screened with 17 primers and made to score polymorphism. The main emphasis of the present study was to assess the genetic diversity at intra specific level among the 3 accessions of P. pelagicus species of Gulf of Mannarusing RAPD markers. RAPD analysis shows that there is a high level of polymorphism among different accessions. From this study, it was understood that each location varied with respect to environmental factors and genetic parameters. The OPB-18, OPB-19, OPC-07 and OPN-06 primers produced distinct, highly reproducible amplification profile for all the screened samples. In the present study, amplification bands ranged between 250 and 663 bp. Maximum numbers of bands were produced by OPN-06 and least by OPB-19. Moderate to high genetic diversity was observed in all geographic samples of P. pelagicus from RAPD analysis. RAPD analysis from three different geographical regions shows clear polymorphic patterns. Thoothukudi and Rameshwaram populations appear in one cluster, while the Kanyakumari populations formed the other cluster indicating a genetic variability and diversity in samples collected from different places.

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